Unified Statistical Modeling of Omics Data
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Documentation for package ‘autonomics’ version 1.14.6
Help Pages
A B C D E F G H I K L M N O P Q R S T U V W X Z misc
-- A --
| ABBREV_TO_ORGNAME | Annotation Maps |
| abstractvar | Get model variable |
| abstractvar.data.table | Get model variable |
| abstractvar.SummarizedExperiment | Get model variable |
| abstractvec | Get model variable |
| abstractvec.data.table | Get model variable |
| abstractvec.SummarizedExperiment | Get model variable |
| abstract_fit | Abstract model fit |
| add_adjusted_pvalues | Add adjusted pvalues |
| add_assay_means | Add assay means |
| add_facetvars | Add facetvars |
| add_opentargets_by_uniprot | Add opentargets annotations |
| add_psp | Add psp |
| add_smiles | Add smiles |
| altenrich | Alternative Enrichment Analysis |
| analysis | Get/set analysis |
| analysis-method | Get/set analysis |
| analysis<- | Get/set analysis |
| analysis<--method | Get/set analysis |
| analyze | Analyze |
| annotate_maxquant | Annotate maxquant |
| annotate_uniprot_rest | Annotate uniprot/ensp |
| assert_compounddiscoverer_output | Is diann, fragpipe, proteingroups, phosphosites file? |
| assert_correlation_matrix | Assert correlation matrix |
| assert_diann_report | Is diann, fragpipe, proteingroups, phosphosites file? |
| assert_fastadt | Is fastadt |
| assert_fragpipe_tsv | Is diann, fragpipe, proteingroups, phosphosites file? |
| assert_is_fraction | Is fraction |
| assert_is_valid_sumexp | Assert that x is a valid SummarizedExperiment |
| assert_maxquant_phosphosites | Is diann, fragpipe, proteingroups, phosphosites file? |
| assert_maxquant_proteingroups | Is diann, fragpipe, proteingroups, phosphosites file? |
| assert_positive_number | Is positive number |
| assert_scalar_subset | Is scalar subset |
| assert_valid_formula | Is valid formula |
| assert_weakly_positive_number | Is positive number |
| AUTONOMICS_DATASETS | Data used in examples/vignette/tests/longtests |
-- B --
| beta | Model based prediction |
| bin | Bin continuous variable |
| bin.character | Bin continuous variable |
| bin.factor | Bin continuous variable |
| bin.logical | Bin continuous variable |
| bin.numeric | Bin continuous variable |
| bin.SummarizedExperiment | Bin continuous variable |
| biplot | Biplot |
| biplot_corrections | Biplot batch corrections |
| biplot_covariates | Biplot covariates |
| block2lme | Put block in lme-compatible format |
| block2lme.character | Put block in lme-compatible format |
| block2lme.formula | Put block in lme-compatible format |
| block2lme.list | Put block in lme-compatible format |
| block_vars | Put block in lme-compatible format |
-- C --
| cbind_imputed | Split samples |
| center | Center samples |
| code | Contrast Code Factor |
| code.data.table | Contrast Code Factor |
| code.factor | Contrast Code Factor |
| code_control | Contrast Code Factor |
| code_deviation | Contrast Code Factor |
| code_deviation_first | Contrast Code Factor |
| code_diff | Contrast Code Factor |
| code_diff_forward | Contrast Code Factor |
| code_helmert | Contrast Code Factor |
| code_helmert_forward | Contrast Code Factor |
| coefs | Get coefs |
| coefs.data.table | Get coefs |
| coefs.factor | Get coefs |
| coefs.SummarizedExperiment | Get coefs |
| collapsed_entrezg_to_symbol | Collapsed entrezg to genesymbol |
| collapse_in | Count/Collapse in/outside intersection |
| collapse_in.character | Count/Collapse in/outside intersection |
| collapse_in.factor | Count/Collapse in/outside intersection |
| collapse_in.list | Count/Collapse in/outside intersection |
| COMPOUNDDISCOVERER_PATTERNS | compound discoverer quantity patterns |
| CONTAMINANTSURL | Contaminants URL |
| contr.diff | Contrast Code Factor |
| contr.treatment.explicit | Contrast Code Factor |
| contrast_subgroup_cols | Row/Col contrasts |
| contrast_subgroup_rows | Row/Col contrasts |
| counts | Get/Set counts |
| counts-method | Get/Set counts |
| counts2cpm | Convert between counts and cpm/tpm |
| counts2tpm | counts to tpm |
| counts<- | Get/Set counts |
| counts<--method | Get/Set counts |
| count_in | Count/Collapse in/outside intersection |
| count_in.character | Count/Collapse in/outside intersection |
| count_in.factor | Count/Collapse in/outside intersection |
| count_in.list | Count/Collapse in/outside intersection |
| count_out | Count/Collapse in/outside intersection |
| count_out.character | Count/Collapse in/outside intersection |
| count_out.factor | Count/Collapse in/outside intersection |
| count_out.list | Count/Collapse in/outside intersection |
| cpm | Get/Set cpm |
| cpm-method | Get/Set cpm |
| cpm2counts | Convert between counts and cpm/tpm |
| cpm<- | Get/Set cpm |
| cpm<--method | Get/Set cpm |
| create_design | Create design matrix |
| create_design.data.table | Create design matrix |
| create_design.SummarizedExperiment | Create design matrix |
-- D --
| DATADIR | Download autonomics example data |
| default_coefs | Get default coefs |
| default_coefs.data.table | Get default coefs |
| default_coefs.SummarizedExperiment | Get default coefs |
| default_formula | Create default formula |
| default_geom | Default geom |
| default_sfile | Default sfile |
| default_subgroupvar | Create default formula |
| demultiplex | Demultiplex snames |
| dequantify | Dequantify maxquant snames |
| dequantify_compounddiscoverer | dequantify_compounddiscoverer compound discoverer snames |
| downfeatures | Get model variable |
| download_contaminants | Downloads contaminants |
| download_data | Download autonomics example data |
| download_gtf | Download GTF file |
| download_mcclain21 | Download mcclain21 data |
| download_tcga_example | Download tcga example |
| dt2mat | 'data.table' to 'matrix' |
-- E --
| effectdt | Get model variable |
| effectmat | Get model variable |
| effectsizemat | Get model variable |
| effectvar | Get model variable |
| effectvec | Get model variable |
| enrichment | Enrichment analysis |
| ens2org | taxon/ens to organism |
| entrezg_to_symbol | Entrezg to genesymbol |
| EXISTENCE_TO_NUMBER | Annotation Maps |
| exp2 | Transform values |
| explore_transformations | Explore transformations |
| extract_coef_features | Extract coefficient features |
| extract_rectangle | Extract rectangle from omics file, data.table, or matrix |
| extract_rectangle.character | Extract rectangle from omics file, data.table, or matrix |
| extract_rectangle.data.table | Extract rectangle from omics file, data.table, or matrix |
| extract_rectangle.matrix | Extract rectangle from omics file, data.table, or matrix |
-- F --
| factor2logical | logical to factor |
| fcluster | Cluster features |
| fcor | Feature correlations/distances |
| fdata | Get/Set sample/feature data |
| fdata-method | Get/Set sample/feature data |
| fdata<- | Get/Set sample/feature data |
| fdata<--method | Get/Set sample/feature data |
| fdist | Feature correlations/distances |
| fdr2p | fdr to p |
| fdrmat | Get model variable |
| fdrvar | Get model variable |
| fdrvec | Get model variable |
| fdt | Get/Set sample/feature data |
| fdt-method | Get/Set sample/feature data |
| fdt<- | Get/Set sample/feature data |
| fdt<--method | Get/Set sample/feature data |
| filter_exprs_replicated_in_some_subgroup | Filter features with replicated expression in some subgroup |
| filter_features | Filter features on condition |
| filter_medoid | Filter medoid sample |
| filter_samples | Filter samples on condition |
| fit | Fit General Linear Model |
| fitcoefs | fitcoefs |
| fitdt | Get fit vars/dt |
| fits | Get fit models |
| fits.data.table | Get fit models |
| fits.SummarizedExperiment | Get fit models |
| FITSEP | Fit results separator |
| fitvars | Get fit vars/dt |
| fit_limma | Fit General Linear Model |
| fit_lm | Fit lm, lme, or lmer |
| fit_lme | Fit lm, lme, or lmer |
| fit_lmer | Fit lm, lme, or lmer |
| fit_lmx | Fit lm, lme, or lmer |
| fit_survival | Fit/Plot survival |
| fit_wilcoxon | Fit General Linear Model |
| fix_xlgenes | Fix excel genes |
| flevels | Get fvar levels |
| fnames | Get/Set fnames |
| fnames-method | Get/Set fnames |
| fnames<- | Get/Set fnames |
| fnames<--method | Get/Set fnames |
| formula2lm | Put block in lme-compatible format |
| formula2lmer | Put block in lme-compatible format |
| formula2str | formula to string |
| fscale | Transform values |
| ftype | Feature type |
| fvalues | Get fvalues |
| fvars | Get/Set fvars |
| fvars-method | Get/Set fvars |
| fvars<- | Get/Set fvars |
| fvars<--method | Get/Set fvars |
-- G --
| genome_to_orgdb | Get corresponding orgdb |
| group_by_level | group by level |
| group_by_level.character | group by level |
| group_by_level.data.table | group by level |
| group_by_level.factor | group by level |
| guess_compounddiscoverer_quantity | Guess compound discoverer quantity from snames |
| guess_fitsep | guess fitsep |
| guess_fitsep.data.table | guess fitsep |
| guess_fitsep.SummarizedExperiment | guess fitsep |
| guess_maxquant_quantity | Guess maxquant quantity from snames |
| guess_sep | Guess separator |
| guess_sep.character | Guess separator |
| guess_sep.factor | Guess separator |
| guess_sep.numeric | Guess separator |
| guess_sep.SummarizedExperiment | Guess separator |
-- H --
| has_multiple_levels | Variable has multiple levels? |
| has_multiple_levels.character | Variable has multiple levels? |
| has_multiple_levels.data.table | Variable has multiple levels? |
| has_multiple_levels.factor | Variable has multiple levels? |
| has_multiple_levels.numeric | Variable has multiple levels? |
| has_multiple_levels.SummarizedExperiment | Variable has multiple levels? |
| hdlproteins | hdl proteomewatch proteins |
-- I --
| impute | Impute |
| impute.matrix | Impute |
| impute.numeric | Impute |
| impute.SummarizedExperiment | Impute |
| inf_to_na | Change nondetect representation |
| invert_subgroups | Invert subgroups |
| invnorm | Transform values |
| is_collapsed_subset | Is collapsed subset |
| is_compounddiscoverer_output | Is diann, fragpipe, proteingroups, phosphosites file? |
| is_correlation_matrix | Assert correlation matrix |
| is_diann_report | Is diann, fragpipe, proteingroups, phosphosites file? |
| is_fastadt | Is fastadt |
| is_file | Is a file? |
| is_fraction | Is fraction |
| is_fragpipe_tsv | Is diann, fragpipe, proteingroups, phosphosites file? |
| is_imputed | Get/set is_imputed |
| is_imputed-method | Get/set is_imputed |
| is_imputed<- | Get/set is_imputed |
| is_imputed<--method | Get/set is_imputed |
| is_maxquant_phosphosites | Is diann, fragpipe, proteingroups, phosphosites file? |
| is_maxquant_proteingroups | Is diann, fragpipe, proteingroups, phosphosites file? |
| is_positive_number | Is positive number |
| is_scalar_subset | Is scalar subset |
| is_sig | Is significant? |
| is_valid_formula | Is valid formula |
| is_weakly_positive_number | Is positive number |
-- K --
| keep_connected_blocks | Keep fully connected blocks |
| keep_connected_features | Keep features with n+ connected blocks |
| keep_replicated_features | Keep replicated features |
-- L --
| label2index | Convert labels into indices |
| lda | PCA, SMA, LDA, PLS, SPLS, OPLS |
| LINMOD_ENGINES | Linear Modeling Engines |
| list2mat | list to matrix |
| list_files | list files |
| loadingmat | Extract scores/loadings |
| loadings | Extract scores/loadings |
| log2counts | Get/Set log2counts |
| log2counts-method | Get/Set log2counts |
| log2counts<- | Get/Set log2counts |
| log2counts<--method | Get/Set log2counts |
| log2cpm | Get/Set log2cpm |
| log2cpm-method | Get/Set log2cpm |
| log2cpm<- | Get/Set log2cpm |
| log2cpm<--method | Get/Set log2cpm |
| log2diffs | Get/Set log2diffs |
| log2diffs-method | Get/Set log2diffs |
| log2diffs<- | Get/Set log2diffs |
| log2diffs<--method | Get/Set log2diffs |
| log2proteins | Get/Set log2proteins |
| log2proteins-method | Get/Set log2proteins |
| log2proteins<- | Get/Set log2proteins |
| log2proteins<--method | Get/Set log2proteins |
| log2sites | Get/Set log2sites |
| log2sites-method | Get/Set log2sites |
| log2sites<- | Get/Set log2sites |
| log2sites<--method | Get/Set log2sites |
| log2tpm | Get/Set log2tpm |
| log2tpm-method | Get/Set log2tpm |
| log2tpm<- | Get/Set log2tpm |
| log2tpm<--method | Get/Set log2tpm |
| log2transform | Transform values |
| logical2factor | logical to factor |
-- M --
| make_alpha_palette | Make alpha palette |
| make_colors | Make colors |
| make_volcano_dt | Create volcano datatable |
| map_fvalues | Map fvalues |
| mat2dt | 'data.table' to 'matrix' |
| matrix2sumexp | Convert matrix into SummarizedExperiment |
| MAXQUANT_PATTERNS | maxquant quantity patterns |
| mdsplot | Feature correlations/distances |
| merge_compounddiscoverer | merge compound discoverer files |
| merge_fdata | Merge sample/feature dt |
| merge_fdt | Merge sample/feature dt |
| merge_ffile | Merge sample / feature file |
| merge_sample_excel | Merge sample excel |
| merge_sample_file | Merge sample / feature file |
| merge_sdata | Merge sample/feature dt |
| merge_sdt | Merge sample/feature dt |
| message_df | message dataframe |
| minusinf_to_na | Change nondetect representation |
| modeldt | Get model variable |
| modeldt.data.table | Get model variable |
| modeldt.SummarizedExperiment | Get model variable |
| modelfeatures | Get model variable |
| modelfeatures.data.table | Get model variable |
| modelfeatures.SummarizedExperiment | Get model variable |
| modelmat | Get model variable |
| modelvar | Get model variable |
| modelvar.data.table | Get model variable |
| modelvar.SummarizedExperiment | Get model variable |
| modelvec | Get model variable |
| modelvec.data.table | Get model variable |
| modelvec.SummarizedExperiment | Get model variable |
| MSIGCOLLECTIONSHUMAN | Human/Mouse Msigdb Collections |
| MSIGCOLLECTIONSMOUSE | Human/Mouse Msigdb Collections |
| MSIGDIR | local msigdb dir |
-- N --
| nan_to_na | Change nondetect representation |
| na_to_string | Change nondetect representation |
| na_to_zero | Change nondetect representation |
| nfactors | stri_split and extract |
| no_nas | Is systematic/random/full NA |
-- O --
| OPENTARGETSDIR | opentargets dir |
| opls | PCA, SMA, LDA, PLS, SPLS, OPLS |
| order_on_effect | Order on p |
| order_on_p | Order on p |
-- P --
| parse_maxquant_hdrs | Read fasta hdrs |
| pca | PCA, SMA, LDA, PLS, SPLS, OPLS |
| pdt | Get model variable |
| percentiles | survival percentiles |
| pg_to_canonical | proteingroup to isoforms |
| pg_to_isoforms | proteingroup to isoforms |
| plot_contrastogram | Plot contrastogram |
| plot_contrast_venn | Plot contrast venn |
| plot_data | Plot data |
| plot_densities | Plot sample/feature distributions |
| plot_design | Plot model |
| plot_detections | Plot missingness per sample / subgroup |
| plot_exprs | Plot exprs for coef |
| plot_exprs_per_coef | Plot exprs per coef |
| plot_feature_boxplots | Plot exprs for coef |
| plot_feature_densities | Plot sample/feature distributions |
| plot_feature_violins | Plot sample/feature violins |
| plot_fit_summary | Plot fit summary |
| plot_heatmap | Plot heatmap |
| plot_matrix | Plot binary matrix |
| plot_sample_boxplots | Plot exprs for coef |
| plot_sample_densities | Plot sample/feature distributions |
| plot_sample_nas | Plot missingness per sample / subgroup |
| plot_sample_violins | Plot sample/feature violins |
| plot_subgroup_nas | Plot missingness per sample / subgroup |
| plot_subgroup_points | Plot features |
| plot_subgroup_violins | Plot sample/feature violins |
| plot_summarized_detections | Plot missingness per sample / subgroup |
| plot_summary | Plot summary |
| plot_survival | Fit/Plot survival |
| plot_venn | Plot venn |
| plot_venn_heatmap | Plot venn heatmap |
| plot_violins | Plot sample/feature violins |
| plot_volcano | Plot volcano |
| pls | PCA, SMA, LDA, PLS, SPLS, OPLS |
| pmat | Get model variable |
| PPATTERN | Fit results separator |
| PRECURSOR_QUANTITY | diann precursor quantity |
| preprocess_rnaseq_counts | Preprocess RNAseq counts |
| pull_columns | Pull columns in a dataframe to the front |
| pvar | Get model variable |
| pvec | Get model variable |
-- Q --
| quantnorm | Transform values |
-- R --
| random_nas | Is systematic/random/full NA |
| read_affymetrix | Read affymetrix microarray |
| read_compounddiscoverer | Read compound discoverer output |
| read_contaminantdt | Read fasta hdrs |
| read_contaminants | Read contaminants |
| read_diann | Read diann |
| read_diann_proteingroups | Read diann |
| read_fragpipe | Read fragpipe |
| read_maxquant_phosphosites | Read maxquant phosphosites |
| read_maxquant_proteingroups | Read maxquant proteingroups |
| read_metabolon | Read metabolon xlsxfile |
| read_msigdt | Read msigdb datatable |
| read_olink | Read olink file |
| read_phosphosites | Read maxquant phosphosites |
| read_proteingroups | Read maxquant proteingroups |
| read_rectangles | Read omics data from rectangular file |
| read_rnaseq_bams | Read rnaseq counts/bams |
| read_rnaseq_counts | Read rnaseq counts/bams |
| read_salmon | Read salmon |
| read_somascan | Read somascan adatfile |
| read_uniprotdt | Read fasta hdrs |
| recollapse | Uncollapse/Recollapse |
| reset_fit | Reset fit |
| REVIEWED_TO_NUMBER | Annotation Maps |
| rm_diann_contaminants | Rm contaminants |
| rm_missing_in_all_samples | Rm features missing in some samples |
| rm_missing_in_some_samples | Rm features missing in some samples |
| rm_singleton_samples | rm unmatched/singleton samples |
| rm_unmatched_samples | rm unmatched/singleton samples |
-- S --
| sampleid_values | Get/Set svalues |
| scaledlibsizes | Get tmm-scaled libsizes |
| scor | Feature correlations/distances |
| scoremat | Extract scores/loadings |
| scores | Extract scores/loadings |
| sdata | Get/Set sample/feature data |
| sdata-method | Get/Set sample/feature data |
| sdata<- | Get/Set sample/feature data |
| sdata<--method | Get/Set sample/feature data |
| sdist | Feature correlations/distances |
| sdt | Get/Set sample/feature data |
| sdt-method | Get/Set sample/feature data |
| sdt<- | Get/Set sample/feature data |
| sdt<--method | Get/Set sample/feature data |
| slevels | Get slevels |
| sma | PCA, SMA, LDA, PLS, SPLS, OPLS |
| snames | Get/Set snames |
| snames-method | Get/Set snames |
| snames<- | Get/Set snames |
| snames<--method | Get/Set snames |
| split_extract | stri_split and extract |
| split_extract_fixed | stri_split and extract |
| split_extract_regex | stri_split and extract |
| split_features | Split samples |
| split_samples | Split samples |
| spls | PCA, SMA, LDA, PLS, SPLS, OPLS |
| sscale | Transform values |
| stri_any_regex | Does any string have a regex |
| stri_detect_fixed_in_collapsed | Detect fixed patterns in collapsed strings |
| subgroup_array | Get subgroup matrix |
| subgroup_levels | Get slevels |
| subgroup_matrix | Get subgroup matrix |
| subgroup_values | Get/Set svalues |
| subtract_baseline | Subtract baseline |
| subtract_differences | Subtract baseline |
| subtract_pairs | Subtract baseline |
| sumexplist_to_longdt | SummarizedExperiment list to long data.table |
| sumexp_to_longdt | SummarizedExperiment to data.table |
| sumexp_to_subrep_dt | SummarizedExperiment to data.table |
| sumexp_to_tsv | Write sumexp to tsv |
| sumexp_to_widedt | SummarizedExperiment to data.table |
| summarize_fit | Summarize fit |
| summarize_fit.data.table | Summarize fit |
| summarize_fit.SummarizedExperiment | Summarize fit |
| svalues | Get/Set svalues |
| svalues<- | Get/Set svalues |
| svalues<--method | Get/Set svalues |
| svars | Get/Set svars |
| svars-method | Get/Set svars |
| svars<- | Get/Set svars |
| svars<--method | Get/Set svars |
| systematic_nas | Is systematic/random/full NA |
-- T --
| tag_features | Tag features |
| tag_hdlproteins | Tag hdlproteins |
| taxon2org | taxon/ens to organism |
| TAXON_TO_ORGNAME | Annotation Maps |
| tdt | Get model variable |
| TESTS | Statistical models supported in autonomics |
| tmat | Get model variable |
| tpm | Get/Set tpm |
| tpm-method | Get/Set tpm |
| tpm<- | Get/Set tpm |
| tpm<--method | Get/Set tpm |
| tvar | Get model variable |
| tvec | Get model variable |
| twofactor_sumexp | twofactor sumexp |
-- U --
| uncollapse | Uncollapse/Recollapse |
| upfeatures | Get model variable |
-- V --
| values | Get/Set expr values |
| values-method | Get/Set expr values |
| values<- | Get/Set expr values |
| values<--method | Get/Set expr values |
| varlevels_dont_clash | Are varlevels unique |
| varlevels_dont_clash.data.table | Are varlevels unique |
| varlevels_dont_clash.SummarizedExperiment | Are varlevels unique |
| venn_detects | Venn detects |
| vsn | Transform values |
-- W --
| weights | Get/Set weights |
| weights-method | Get/Set weights |
| weights<- | Get/Set weights |
| weights<--method | Get/Set weights |
| write_ods | Write xl/ods |
| write_xl | Write xl/ods |
-- X --
| X | Model based prediction |
-- Z --
| zero_to_na | Change nondetect representation |
| zscore | Transform values |
-- misc --
| .extract_effectsize_features | Extract coefficient features |
| .extract_fdr_features | Extract coefficient features |
| .extract_n_features | Extract coefficient features |
| .extract_p_features | Extract coefficient features |
| .extract_sign_features | Extract coefficient features |
| .fit_limma | Fit General Linear Model |
| .merge | Clean Merge |
| .plot_survival | Fit/Plot survival |
| .read_compounddiscoverer | Read compound discoverer files as-is |
| .read_diann_precursors | Read diann |
| .read_diann_proteingroups | Read diann |
| .read_maxquant_phosphosites | Read proteingroups/phosphosites as-is |
| .read_maxquant_proteingroups | Read proteingroups/phosphosites as-is |
| .read_metabolon | Read metabolon xlsxfile |
| .read_rectangles | Read omics data from rectangular file |
| .read_rnaseq_bams | Read rnaseq counts/bams |
| .read_rnaseq_counts | Read rnaseq counts/bams |
| .read_somascan | Read somascan adatfile |