This vignette summarizes the functionalities and options of MSstastTMTPTM and provides a workflow example.
MSstatsTMTPTM includes the following two functions for data visualization and statistical testing:
dataProcessPlotsTMTPMTgroupComparisonTMTPTMTo install this package, start R (version “4.0”) and enter:
To illustrate the quantitative data and quality control of MS runs, dataProcessPlotsTMT takes the quantitative data from MSstatsTMT converter functions as input and generate two types of figures in pdf files as output : 1. Profile plot (specify “ProfilePlot” in option type), to identify the potential sources of variation for each protein; 2. Quality control plot (specify “QCPlot” in option type), to evaluate the systematic bias between MS runs.
data.ptm name of the data with PTM sites in protein name, which can be the output of MSstatsTMT converter functions.data.protein name of the data with peptide level, which can be the output of MSstatsTMT converter functions.data.ptm.summarization name of the data with ptm sites in protein-level name , which can be the output of the MSstatsTMT function.data.protein.summarization name of the data with protein-level, which can be the output of the MSstatsTMT function.type choice of visualization. “ProfilePlot” represents profile plot of log intensities across MS runs. “QCPlot” represents box plots of log intensities across channels and MS runs.ylimUp upper limit for y-axis in the log scale. FALSE(Default) for Profile Plot and QC Plot uses the upper limit as rounded off maximum of log2(intensities) after normalization + 3..ylimDown lower limit for y-axis in the log scale. FALSE(Default) for Profile Plot and QC Plot uses 0..x.axis.size size of x-axis labeling for “Run” and "channel in Profile Plot and QC Plot.y.axis.size size of y-axis labels. Default is 10.text.size size of labels represented each condition at the top of Profile plot and QC plot. Default is 4.text.angle angle of labels represented each condition at the top of Profile plot and QC plot. Default is 0.legend.size size of legend above Profile plot. Default is 7.dot.size.profile size of dots in Profile plot. Default is 2.ncol.guide number of columns for legends at the top of plot. Default is 5.width width of the saved pdf file. Default is 10.height height of the saved pdf file. Default is 10.which.Protein Protein list to draw plots. List can be names of Proteins or order numbers of Proteins. Default is “all”, which generates all plots for each protein. For QC plot, “allonly” will generate one QC plot with all proteins.originalPlot TRUE(default) draws original profile plots, without normalization.summaryPlot TRUE(default) draws profile plots with protein summarization for each channel and MS run.address the name of folder that will store the results. Default folder is the current working directory. The other assigned folder has to be existed under the current working directory. An output pdf file is automatically created with the default name of “ProfilePlot.pdf” or “QCplot.pdf”. The command address can help to specify where to store the file as well as how to modify the beginning of the file name. If address=FALSE, plot will be not saved as pdf file but showed in window.The raw dataset for both the PTM and Protein datasets are required for the plotting function. This can be the output of the MSstatsTMT converter functions: PDtoMSstatsTMTFormat, SpectroMinetoMSstatsTMTFormat, and OpenMStoMSstatsTMTFormat. Both the PTM and protein datasets must include the following columns: ProteinName, PeptideSequence, Charge, PSM, Mixture, TechRepMixture, Run, Channel, Condition, BioReplicate, and Intensity.
# read in raw data files
# raw.ptm <- read.csv(file="raw.ptm.csv", header=TRUE)
# raw.protein <- read.csv(file="raw.protein.csv", header=TRUE)
head(raw.ptm)
#> ProteinName PeptideSequence Charge PSM Mixture TechRepMixture
#> 1 Protein_12_S703 Peptide_491 3 Peptide_491_3 1 1
#> 2 Protein_12_S703 Peptide_491 3 Peptide_491_3 1 1
#> 3 Protein_12_S703 Peptide_491 3 Peptide_491_3 1 1
#> 4 Protein_12_S703 Peptide_491 3 Peptide_491_3 1 1
#> 5 Protein_12_S703 Peptide_491 3 Peptide_491_3 1 1
#> 6 Protein_12_S703 Peptide_491 3 Peptide_491_3 1 1
#> Run Channel Condition BioReplicate Intensity
#> 1 1_1 128N Condition_2 Condition_2_1 48030.0
#> 2 1_1 129C Condition_4 Condition_4_2 100224.4
#> 3 1_1 131C Condition_3 Condition_3_2 66804.6
#> 4 1_1 130N Condition_1 Condition_1_2 46779.8
#> 5 1_1 128C Condition_6 Condition_6_1 77497.9
#> 6 1_1 126C Condition_4 Condition_4_1 81559.7
head(raw.protein)
#> ProteinName PeptideSequence Charge PSM Mixture TechRepMixture Run
#> 1 Protein_12 Peptide_9121 3 Peptide_9121_3 1 1 1_1
#> 2 Protein_12 Peptide_27963 5 Peptide_27963_5 1 1 1_1
#> 3 Protein_12 Peptide_28482 4 Peptide_28482_4 1 1 1_1
#> 4 Protein_12 Peptide_10940 2 Peptide_10940_2 2 1 2_1
#> 5 Protein_12 Peptide_4900 2 Peptide_4900_2 2 1 2_1
#> 6 Protein_12 Peptide_4900 3 Peptide_4900_3 2 1 2_1
#> Channel Condition BioReplicate Intensity
#> 1 126C Condition_4 Condition_4_1 10996116.9
#> 2 127C Condition_5 Condition_5_1 56965.1
#> 3 131N Condition_2 Condition_2_2 286121.7
#> 4 131N Condition_2 Condition_2_4 534806.0
#> 5 126C Condition_4 Condition_4_3 1134908.7
#> 6 126C Condition_4 Condition_4_3 1605773.2# Run MSstatsTMT proteinSummarization function
quant.msstats.ptm <- proteinSummarization(raw.ptm,
method = "msstats",
global_norm = TRUE,
reference_norm = FALSE,
MBimpute = TRUE)
quant.msstats.protein <- proteinSummarization(raw.protein,
method = "msstats",
global_norm = TRUE,
reference_norm = FALSE,
MBimpute = TRUE)head(quant.msstats.ptm)
#> Run Protein Abundance Channel BioReplicate Condition
#> 1 1_1 Protein_1076_Y67 13.65475 130N Condition_1_2 Condition_1
#> 2 1_1 Protein_1076_Y67 13.57146 127N Condition_1_1 Condition_1
#> 3 1_1 Protein_1076_Y67 13.56900 128N Condition_2_1 Condition_2
#> 4 1_1 Protein_1076_Y67 13.70567 131N Condition_2_2 Condition_2
#> 5 1_1 Protein_1076_Y67 13.24717 131C Condition_3_2 Condition_3
#> 6 1_1 Protein_1076_Y67 13.11874 129N Condition_3_1 Condition_3
#> TechRepMixture Mixture
#> 1 1 1
#> 2 1 1
#> 3 1 1
#> 4 1 1
#> 5 1 1
#> 6 1 1
head(quant.msstats.protein)
#> Run Protein Abundance Channel BioReplicate Condition TechRepMixture
#> 1 1_1 Protein_1076 18.75131 127N Condition_1_1 Condition_1 1
#> 2 1_1 Protein_1076 18.80198 130N Condition_1_2 Condition_1 1
#> 3 1_1 Protein_1076 18.92222 131N Condition_2_2 Condition_2 1
#> 4 1_1 Protein_1076 19.02252 128N Condition_2_1 Condition_2 1
#> 5 1_1 Protein_1076 18.28685 131C Condition_3_2 Condition_3 1
#> 6 1_1 Protein_1076 18.40555 129N Condition_3_1 Condition_3 1
#> Mixture
#> 1 1
#> 2 1
#> 3 1
#> 4 1
#> 5 1
#> 6 1
# Profile Plot
dataProcessPlotsTMTPTM(data.ptm=raw.ptm,
data.protein=raw.protein,
data.ptm.summarization=quant.msstats.ptm,
data.protein.summarization=quant.msstats.protein,
type='ProfilePlot'
)
#> Warning: Removed 275 rows containing missing values (geom_point).
#> Warning: Removed 275 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_12_S703 ( 1 of 89 )
#> Drew the Profile plot for Protein_15_S140 ( 2 of 89 )
#> Drew the Profile plot for Protein_15_Y137 ( 3 of 89 )
#> Warning: Removed 484 rows containing missing values (geom_point).
#> Warning: Removed 484 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_125_Y343 ( 4 of 89 )
#> Warning: Removed 1045 rows containing missing values (geom_point).
#> Warning: Removed 1045 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_150_S729 ( 5 of 89 )
#> Drew the Profile plot for Protein_152_S455 ( 6 of 89 )
#> Warning: Removed 121 rows containing missing values (geom_point).
#> Warning: Removed 121 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_191_S679 ( 7 of 89 )
#> Warning: Removed 341 rows containing missing values (geom_point).
#> Warning: Removed 341 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_261_S637 ( 8 of 89 )
#> Warning: Removed 341 rows containing missing values (geom_point).
#> Warning: Removed 341 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_261_S180 ( 9 of 89 )
#> Warning: Removed 341 rows containing missing values (geom_point).
#> Warning: Removed 341 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_261_S182 ( 10 of 89 )
#> Drew the Profile plot for Protein_320_S198 ( 11 of 89 )
#> Warning: Removed 748 rows containing missing values (geom_point).
#> Warning: Removed 748 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_324_S122 ( 12 of 89 )
#> Warning: Removed 396 rows containing missing values (geom_point).
#> Warning: Removed 396 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_541_S504 ( 13 of 89 )
#> Warning: Removed 121 rows containing missing values (geom_point).
#> Warning: Removed 121 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_843_S295 ( 14 of 89 )
#> Warning: Removed 33 rows containing missing values (geom_point).
#> Warning: Removed 33 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_971_S326 ( 15 of 89 )
#> Drew the Profile plot for Protein_1076_Y67 ( 16 of 89 )
#> Warning: Removed 132 rows containing missing values (geom_point).
#> Warning: Removed 132 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1145_T915 ( 17 of 89 )
#> Drew the Profile plot for Protein_1146_S328 ( 18 of 89 )
#> Warning: Removed 154 rows containing missing values (geom_point).
#> Warning: Removed 154 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1160_S188 ( 19 of 89 )
#> Drew the Profile plot for Protein_1220_Y321 ( 20 of 89 )
#> Warning: Removed 99 rows containing missing values (geom_point).
#> Warning: Removed 99 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1235_S416 ( 21 of 89 )
#> Drew the Profile plot for Protein_1326_Y182 ( 22 of 89 )
#> Drew the Profile plot for Protein_1380_Y106 ( 23 of 89 )
#> Drew the Profile plot for Protein_1547_Y608 ( 24 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1548_Y849 ( 25 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1548_Y580 ( 26 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1548_T850 ( 27 of 89 )
#> Warning: Removed 66 rows containing missing values (geom_point).
#> Warning: Removed 66 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1551_S994 ( 28 of 89 )
#> Warning: Removed 99 rows containing missing values (geom_point).
#> Warning: Removed 99 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1584_S71 ( 29 of 89 )
#> Drew the Profile plot for Protein_1587_Y168 ( 30 of 89 )
#> Warning: Removed 297 rows containing missing values (geom_point).
#> Warning: Removed 297 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1612_S296 ( 31 of 89 )
#> Warning: Removed 231 rows containing missing values (geom_point).
#> Warning: Removed 231 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1616_S203 ( 32 of 89 )
#> Drew the Profile plot for Protein_1686_T133 ( 33 of 89 )
#> Drew the Profile plot for Protein_1721_S24 ( 34 of 89 )
#> Warning: Removed 297 rows containing missing values (geom_point).
#> Warning: Removed 297 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1739_S237 ( 35 of 89 )
#> Drew the Profile plot for Protein_1852_Y342 ( 36 of 89 )
#> Warning: Removed 330 rows containing missing values (geom_point).
#> Warning: Removed 330 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1863_S2029 ( 37 of 89 )
#> Warning: Removed 330 rows containing missing values (geom_point).
#> Warning: Removed 330 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1863_S2030 ( 38 of 89 )
#> Warning: Removed 22 rows containing missing values (geom_point).
#> Warning: Removed 22 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1864_Y207 ( 39 of 89 )
#> Warning: Removed 22 rows containing missing values (geom_point).
#> Warning: Removed 22 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1864_Y50 ( 40 of 89 )
#> Warning: Removed 22 rows containing missing values (geom_point).
#> Warning: Removed 22 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1864_Y409 ( 41 of 89 )
#> Warning: Removed 286 rows containing missing values (geom_point).
#> Warning: Removed 286 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1865_Y153 ( 42 of 89 )
#> Warning: Removed 110 rows containing missing values (geom_point).
#> Warning: Removed 110 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1929_Y323 ( 43 of 89 )
#> Warning: Removed 154 rows containing missing values (geom_point).
#> Warning: Removed 154 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_1945_Y628 ( 44 of 89 )
#> Drew the Profile plot for Protein_2084_Y44 ( 45 of 89 )
#> Drew the Profile plot for Protein_2108_Y281 ( 46 of 89 )
#> Drew the Profile plot for Protein_2207_S674 ( 47 of 89 )
#> Warning: Removed 2956 rows containing missing values (geom_point).
#> Warning: Removed 2956 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2212_S2980 ( 48 of 89 )
#> Drew the Profile plot for Protein_2215_S568 ( 49 of 89 )
#> Warning: Removed 55 rows containing missing values (geom_point).
#> Warning: Removed 55 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2234_S459 ( 50 of 89 )
#> Warning: Removed 77 rows containing missing values (geom_point).
#> Warning: Removed 77 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2273_Y148 ( 51 of 89 )
#> Warning: Removed 121 rows containing missing values (geom_point).
#> Warning: Removed 121 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2284_Y519 ( 52 of 89 )
#> Warning: Removed 121 rows containing missing values (geom_point).
#> Warning: Removed 121 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2284_Y520 ( 53 of 89 )
#> Drew the Profile plot for Protein_2297_Y276 ( 54 of 89 )
#> Drew the Profile plot for Protein_2297_T279 ( 55 of 89 )
#> Warning: Removed 209 rows containing missing values (geom_point).
#> Warning: Removed 209 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2302_Y393 ( 56 of 89 )
#> Warning: Removed 286 rows containing missing values (geom_point).
#> Warning: Removed 286 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2304_S603 ( 57 of 89 )
#> Drew the Profile plot for Protein_2311_S274 ( 58 of 89 )
#> Warning: Removed 220 rows containing missing values (geom_point).
#> Warning: Removed 220 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2315_S105 ( 59 of 89 )
#> Warning: Removed 352 rows containing missing values (geom_point).
#> Warning: Removed 352 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2353_S394 ( 60 of 89 )
#> Warning: Removed 352 rows containing missing values (geom_point).
#> Warning: Removed 352 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2353_S392 ( 61 of 89 )
#> Warning: Removed 88 rows containing missing values (geom_point).
#> Warning: Removed 88 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2361_S54 ( 62 of 89 )
#> Warning: Removed 88 rows containing missing values (geom_point).
#> Warning: Removed 88 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2361_T53 ( 63 of 89 )
#> Warning: Removed 99 rows containing missing values (geom_point).
#> Warning: Removed 99 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2382_S183 ( 64 of 89 )
#> Drew the Profile plot for Protein_2391_Y40 ( 65 of 89 )
#> Drew the Profile plot for Protein_2395_Y306 ( 66 of 89 )
#> Warning: Removed 418 rows containing missing values (geom_point).
#> Warning: Removed 418 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2461_Y250 ( 67 of 89 )
#> Warning: Removed 33 rows containing missing values (geom_point).
#> Warning: Removed 33 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2462_Y332 ( 68 of 89 )
#> Warning: Removed 319 rows containing missing values (geom_point).
#> Warning: Removed 319 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2560_T311 ( 69 of 89 )
#> Warning: Removed 165 rows containing missing values (geom_point).
#> Warning: Removed 165 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2607_S563 ( 70 of 89 )
#> Warning: Removed 44 rows containing missing values (geom_point).
#> Warning: Removed 44 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2697_Y698 ( 71 of 89 )
#> Warning: Removed 1111 rows containing missing values (geom_point).
#> Warning: Removed 1111 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2701_S1106 ( 72 of 89 )
#> Warning: Removed 55 rows containing missing values (geom_point).
#> Warning: Removed 55 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2874_Y59 ( 73 of 89 )
#> Warning: Removed 220 rows containing missing values (geom_point).
#> Warning: Removed 220 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2992_Y118 ( 74 of 89 )
#> Warning: Removed 132 rows containing missing values (geom_point).
#> Warning: Removed 132 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_3027_S111 ( 75 of 89 )
#> Warning: Removed 154 rows containing missing values (geom_point).
#> Warning: Removed 154 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_3273_S518 ( 76 of 89 )
#> Drew the Profile plot for Protein_3486_Y505 ( 77 of 89 )
#> Warning: Removed 330 rows containing missing values (geom_point).
#> Warning: Removed 330 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_3659_S1625 ( 78 of 89 )
#> Warning: Removed 88 rows containing missing values (geom_point).
#> Warning: Removed 88 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4093_S435 ( 79 of 89 )
#> Warning: Removed 1011 rows containing missing values (geom_point).
#> Warning: Removed 1011 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4277_T269 ( 80 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4307_S212 ( 81 of 89 )
#> Warning: Removed 209 rows containing missing values (geom_point).
#> Warning: Removed 209 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4338_S523 ( 82 of 89 )
#> Drew the Profile plot for Protein_4475_Y98 ( 83 of 89 )
#> Warning: Removed 1276 rows containing missing values (geom_point).
#> Warning: Removed 1276 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4494_S1128 ( 84 of 89 )
#> Warning: Removed 1177 rows containing missing values (geom_point).
#> Warning: Removed 1177 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4668_T682 ( 85 of 89 )
#> Warning: Removed 99 rows containing missing values (geom_point).
#> Warning: Removed 99 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2072_Y89 ( 86 of 89 )
#> Warning: Removed 44 rows containing missing values (geom_point).
#> Warning: Removed 44 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_2264_Y64 ( 87 of 89 )
#> Warning: Removed 132 rows containing missing values (geom_point).
#> Warning: Removed 132 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4671_S237 ( 88 of 89 )
#> Warning: Removed 132 rows containing missing values (geom_point).
#> Warning: Removed 132 row(s) containing missing values (geom_path).
#> Drew the Profile plot for Protein_4671_Y236 ( 89 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_12_S703 ( 1 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_15_S140 ( 2 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_15_Y137 ( 3 of 89 )
#> Drew the Profile plot with summarization for Protein_125_Y343 ( 4 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_150_S729 ( 5 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_152_S455 ( 6 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_191_S679 ( 7 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_261_S637 ( 8 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_261_S180 ( 9 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_261_S182 ( 10 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_320_S198 ( 11 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_324_S122 ( 12 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_541_S504 ( 13 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_843_S295 ( 14 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_971_S326 ( 15 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1076_Y67 ( 16 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1145_T915 ( 17 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1146_S328 ( 18 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1160_S188 ( 19 of 89 )
#> Drew the Profile plot with summarization for Protein_1220_Y321 ( 20 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1235_S416 ( 21 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1326_Y182 ( 22 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1380_Y106 ( 23 of 89 )
#> Drew the Profile plot with summarization for Protein_1547_Y608 ( 24 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1548_Y849 ( 25 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1548_Y580 ( 26 of 89 )
#> Drew the Profile plot with summarization for Protein_1548_T850 ( 27 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1551_S994 ( 28 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1584_S71 ( 29 of 89 )
#> Drew the Profile plot with summarization for Protein_1587_Y168 ( 30 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1612_S296 ( 31 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1616_S203 ( 32 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1686_T133 ( 33 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1721_S24 ( 34 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1739_S237 ( 35 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1852_Y342 ( 36 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1863_S2029 ( 37 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1863_S2030 ( 38 of 89 )
#> Drew the Profile plot with summarization for Protein_1864_Y207 ( 39 of 89 )
#> Drew the Profile plot with summarization for Protein_1864_Y50 ( 40 of 89 )
#> Drew the Profile plot with summarization for Protein_1864_Y409 ( 41 of 89 )
#> Drew the Profile plot with summarization for Protein_1865_Y153 ( 42 of 89 )
#> Drew the Profile plot with summarization for Protein_1929_Y323 ( 43 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_1945_Y628 ( 44 of 89 )
#> Drew the Profile plot with summarization for Protein_2084_Y44 ( 45 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2108_Y281 ( 46 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2207_S674 ( 47 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2212_S2980 ( 48 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2215_S568 ( 49 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2234_S459 ( 50 of 89 )
#> Drew the Profile plot with summarization for Protein_2273_Y148 ( 51 of 89 )
#> Drew the Profile plot with summarization for Protein_2284_Y519 ( 52 of 89 )
#> Drew the Profile plot with summarization for Protein_2284_Y520 ( 53 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2297_Y276 ( 54 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2297_T279 ( 55 of 89 )
#> Drew the Profile plot with summarization for Protein_2302_Y393 ( 56 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2304_S603 ( 57 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2311_S274 ( 58 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2315_S105 ( 59 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2353_S394 ( 60 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2353_S392 ( 61 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2361_S54 ( 62 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2361_T53 ( 63 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2382_S183 ( 64 of 89 )
#> Drew the Profile plot with summarization for Protein_2391_Y40 ( 65 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2395_Y306 ( 66 of 89 )
#> Drew the Profile plot with summarization for Protein_2461_Y250 ( 67 of 89 )
#> Drew the Profile plot with summarization for Protein_2462_Y332 ( 68 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2560_T311 ( 69 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2607_S563 ( 70 of 89 )
#> Drew the Profile plot with summarization for Protein_2697_Y698 ( 71 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2701_S1106 ( 72 of 89 )
#> Drew the Profile plot with summarization for Protein_2874_Y59 ( 73 of 89 )
#> Drew the Profile plot with summarization for Protein_2992_Y118 ( 74 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_3027_S111 ( 75 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_3273_S518 ( 76 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_3486_Y505 ( 77 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_3659_S1625 ( 78 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4093_S435 ( 79 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4277_T269 ( 80 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4307_S212 ( 81 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4338_S523 ( 82 of 89 )
#> Drew the Profile plot with summarization for Protein_4475_Y98 ( 83 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4494_S1128 ( 84 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4668_T682 ( 85 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2072_Y89 ( 86 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_2264_Y64 ( 87 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4671_S237 ( 88 of 89 )
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Warning: Removed 11 row(s) containing missing values (geom_path).
#> Warning: Removed 11 rows containing missing values (geom_point).
#> Drew the Profile plot with summarization for Protein_4671_Y236 ( 89 of 89 )
# Quality Control Plot
# dataProcessPlotsTMTPTM(data.ptm=ptm.input.pd,
# data.protein=protein.input.pd,
# data.ptm.summarization=quant.msstats.ptm,
# data.protein.summarization=quant.msstats.protein,
# type='QCPlot')Tests for significant changes in PTM abundance adjusted for global protein abundance across conditions based on a family of linear mixed-effects models in TMT experiment. Experimental design of case-control study (patients are not repeatedly measured) is automatically determined based on proper statistical model.
data.ptm : Name of the output of proteinSummarization function with PTM data. It should have columns named Protein, TechRepMixture, Mixture, Run, Channel, Condition, BioReplicate, Abundance.data.protein : Name of the output of proteinSummarization function with Protein data. It should have columns named Protein, TechRepMixture,Mixture, Run, Channel, Condition, BioReplicate, Abundance.contrast.matrix : Comparison between conditions of interests. 1) default is pairwise, which compare all possible pairs between two conditions.moderated : If moderated = TRUE, then moderated t statistic will be calculated; otherwise, ordinary t statistic will be used.adj.method : adjusted method for multiple comparison. ’BH` is default.# test for all the possible pairs of conditions
model.results.pairwise <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
data.protein=quant.msstats.protein)
#>
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names(model.results.pairwise)
#> [1] "PTM.Model" "Protein.Model" "Adjusted.Model"
head(model.results.pairwise[[1]])
#> Protein Label log2FC SE DF
#> 1 Protein_1076_Y67 Condition_1-Condition_2 0.04713074 0.05264970 15.00000
#> 2 Protein_1076_Y67 Condition_1-Condition_3 0.42262536 0.05712141 15.00008
#> 3 Protein_1076_Y67 Condition_1-Condition_4 0.11835636 0.05264970 15.00000
#> 4 Protein_1076_Y67 Condition_1-Condition_5 0.28875531 0.05264970 15.00000
#> 5 Protein_1076_Y67 Condition_1-Condition_6 0.14293731 0.05712141 15.00008
#> 6 Protein_1076_Y67 Condition_2-Condition_3 0.37549462 0.05712141 15.00008
#> pvalue adj.pvalue issue
#> 1 3.848331e-01 0.6180078006 NA
#> 2 2.223242e-06 0.0001000459 NA
#> 3 4.004178e-02 0.0493665767 NA
#> 4 6.285870e-05 0.0007071603 NA
#> 5 2.439269e-02 0.0439068501 NA
#> 6 8.829044e-06 0.0003973070 NA
# Load specific contrast matrix
#example.contrast.matrix <- read.csv(file="example.contrast.matrix.csv", header=TRUE)
example.contrast.matrix
#> Condition_1 Condition_2 Condition_3 Condition_4 Condition_5 Condition_6
#> 1-4 1.0000000 0.0000000 0.0000000 -1.0000000 0.0000000 0.0000000
#> 2-5 0.0000000 1.0000000 0.0000000 0.0000000 -1.0000000 0.0000000
#> 3-6 0.0000000 0.0000000 1.0000000 0.0000000 0.0000000 -1.0000000
#> 1-3 1.0000000 0.0000000 -1.0000000 0.0000000 0.0000000 0.0000000
#> 2-3 0.0000000 1.0000000 -1.0000000 0.0000000 0.0000000 0.0000000
#> 4-6 0.0000000 0.0000000 0.0000000 1.0000000 0.0000000 -1.0000000
#> 5-6 0.0000000 0.0000000 0.0000000 0.0000000 1.0000000 -1.0000000
#> Partial 0.2500000 0.2500000 -0.5000000 0.2500000 0.2500000 -0.5000000
#> Third 0.3333333 0.3333333 0.3333333 -0.3333333 -0.3333333 -0.3333333
# test for specified condition comparisons only
model.results.contrast <- groupComparisonTMTPTM(data.ptm=quant.msstats.ptm,
data.protein=quant.msstats.protein,
contrast.matrix = example.contrast.matrix)
#>
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names(model.results.contrast)
#> [1] "PTM.Model" "Protein.Model" "Adjusted.Model"
head(model.results.contrast[[1]])
#> Protein Label log2FC SE DF pvalue
#> 1 Protein_1076_Y67 1-4 0.11835636 0.05264970 15.00000 4.004178e-02
#> 2 Protein_1076_Y67 2-5 0.24162457 0.05264970 15.00000 3.544345e-04
#> 3 Protein_1076_Y67 3-6 -0.27968805 0.06173696 15.00028 3.984772e-04
#> 4 Protein_1076_Y67 1-3 0.42262536 0.05712141 15.00008 2.223242e-06
#> 5 Protein_1076_Y67 2-3 0.37549462 0.05712141 15.00008 8.829044e-06
#> 6 Protein_1076_Y67 4-6 0.02458095 0.05712141 15.00008 6.730757e-01
#> adj.pvalue issue
#> 1 0.0493665767 NA
#> 2 0.0020224378 NA
#> 3 0.0071725901 NA
#> 4 0.0001000459 NA
#> 5 0.0003973070 NA
#> 6 0.7530134974 NAsessionInfo()
#> R version 4.0.3 (2020-10-10)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 18.04.5 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.12-bioc/R/lib/libRblas.so
#> LAPACK: /home/biocbuild/bbs-3.12-bioc/R/lib/libRlapack.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] MSstatsTMT_1.8.2 MSstatsTMTPTM_1.0.2
#>
#> loaded via a namespace (and not attached):
#> [1] ggrepel_0.9.1 Rcpp_1.0.6 lattice_0.20-41
#> [4] tidyr_1.1.2 snow_0.4-3 gtools_3.8.2
#> [7] assertthat_0.2.1 digest_0.6.27 foreach_1.5.1
#> [10] R6_2.5.0 plyr_1.8.6 backports_1.2.1
#> [13] evaluate_0.14 ggplot2_3.3.3 pillar_1.4.7
#> [16] gplots_3.1.1 rlang_0.4.10 minqa_1.2.4
#> [19] data.table_1.13.6 nloptr_1.2.2.2 Matrix_1.3-2
#> [22] preprocessCore_1.52.1 rmarkdown_2.6 labeling_0.4.2
#> [25] splines_4.0.3 lme4_1.1-26 statmod_1.4.35
#> [28] stringr_1.4.0 MSstats_3.22.0 munsell_0.5.0
#> [31] broom_0.7.4 compiler_4.0.3 numDeriv_2016.8-1.1
#> [34] xfun_0.21 pkgconfig_2.0.3 lmerTest_3.1-3
#> [37] marray_1.68.0 htmltools_0.5.1.1 doSNOW_1.0.19
#> [40] tidyselect_1.1.0 gridExtra_2.3 tibble_3.0.6
#> [43] codetools_0.2-18 matrixStats_0.58.0 crayon_1.4.1
#> [46] dplyr_1.0.4 MASS_7.3-53.1 bitops_1.0-6
#> [49] grid_4.0.3 nlme_3.1-152 gtable_0.3.0
#> [52] lifecycle_1.0.0 DBI_1.1.1 magrittr_2.0.1
#> [55] scales_1.1.1 KernSmooth_2.23-18 stringi_1.5.3
#> [58] farver_2.0.3 reshape2_1.4.4 limma_3.46.0
#> [61] ellipsis_0.3.1 generics_0.1.0 vctrs_0.3.6
#> [64] boot_1.3-27 iterators_1.0.13 tools_4.0.3
#> [67] glue_1.4.2 purrr_0.3.4 parallel_4.0.3
#> [70] survival_3.2-7 yaml_2.2.1 colorspace_2.0-0
#> [73] caTools_1.18.1 minpack.lm_1.2-1 knitr_1.31