# Batch Effects Quality Control Software

## Documentation for package ‘BatchQC’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

BatchQC | Run BatchQC shiny app
batchqc_explained_variation | Returns a list of explained variation by batch and condition combinations
batch_correct | Batch Correct This function allows you to Add batch corrected count matrix to the SE object
batch_design | This function allows you to make a batch design matrix
batch_indicator | Batch and Condition indicator for signature data
bladder_data_upload | Bladder data upload This function uploads the Bladder data set from the bladderbatch package. This dataset is from bladder cancer data with 22,283 different microarray gene expression data. It has 57 bladder samples with 3 metadata variables (batch, outcome and cancer). It contains 5 batches, 3 cancer types (cancer, biopsy, control), and 5 outcomes (Biopsy, mTCC, sTCC-CIS, sTCC+CIS, and Normal). Batch 1 contains only cancer, 2 has cancer and controls, 3 has only controls, 4 contains only biopsy, and 5 contains cancer and biopsy
check_valid_input | Helper function to check for valid input
color_palette | Color palette
combat_correction | Combat Correction This function applies combat correction to your summarized experiment object
combat_seq_correction | Combat-Seq Correction This function applies combat-seq correction to your summarized experiment object
confound_metrics | Combine std. Pearson correlation coefficient and Cramer's V
cor_props | This function allows you to calculate correlation properties
covariates_not_confounded | Returns list of covariates not confounded by batch; helper function for explained variation and for populating shiny app condition options
cramers_v | This function allows you to calculate Cramer's V
dendrogram_alpha_numeric_check | Dendrogram alpha or numeric checker
dendrogram_color_palette | Dendrogram color palette
dendrogram_plotter | Dendrogram Plot
DE_analyze | Differential Expression Analysis
EV_plotter | This function allows you to plot explained variation
EV_table | EV Table Returns table with percent variation explained for specified number of genes
get.res | Helper function to get residuals
heatmap_num_to_char_converter | Heatmap numeric to character converter
heatmap_plotter | Heatmap Plotter
normalize_SE | This function allows you to add normalized count matrix to the SE object
PCA_plotter | This function allows you to plot PCA
plot_data | This function formats the PCA plot using ggplot
preprocess | Preprocess assay data
process_dendrogram | Process Dendrogram
protein_data | Protein data with 39 protein expression levels
protein_sample_info | Batch and Condition indicator for protein expression data
pval_plotter | P-value Plotter This function allows you to plot p-values of explained variation
pval_summary | Returns summary table for p-values of explained variation
signature_data | Signature data with 1600 gene expression levels
std_pearson_corr_coef | Calculate a standardized Pearson correlation coefficient
summarized_experiment | This function creates a summarized experiment object from count and metadata files uploaded by the user
volcano_plot | Volcano plot