proBatch {proBatch} | R Documentation

## proBatch: A package for diagnostics and correction of batch effects, primarily in proteomics

### Description

The proBatch package contains functions for analyzing and correcting batch effects and other unwanted technical variation from high-thoughput experiments. Although the package has primarily been developed for mass spectrometry proteomics (DIA/SWATH), it should also be applicable to most omic data with minor adaptations. It addresses the following needs:

- prepare the data for analysis

- Visualize batch effects in sample-wide and feature-level;

- Normalize and correct for batch effects.

### Arguments

`df_long` | data frame where each row is a single feature in a single sample. It minimally has a `sample_id_col`, a `feature_id_col` and a `measure_col`, but usually also an `m_score` (in OpenSWATH output result file)
`data_matrix` | features (in rows) vs samples (in columns) matrix, with feature IDs in rownames and file/sample names as colnames. Usually the log transformed version of the original data
`sample_annotation` | data matrix with: `sample_id_col` (this can be repeated as row names) biological covariates technical covariates (batches etc)
`sample_id_col` | name of the column in sample_annotation file, where the filenames (colnames of the data matrix are found)
`batch_col` | column in `sample_annotation` that should be used for batch comparison
`order_col` | column in `sample_annotation` that determines sample order. It is used for certain diagnostics and normalisations.
`measure_col` | if `df_long` is among the parameters, it is the column with expression/abundance/intensity; otherwise, it is used internally for consistency
`feature_id_col` | name of the column with feature/gene/peptide/protein ID used in the long format representation `df_long`. In the wide formatted representation `data_matrix` this corresponds to the row names.
`plot_title` | Title of the plot (usually, processing step + representation level (fragments, transitions, proteins))
`theme` | ggplot theme, by default `classic`. Can be easily overriden

### Details

To learn more about proBatch, start with the vignettes: `browseVignettes(package = "proBatch")`

### Section

Common arguments to the functions.

[Package proBatch version 1.0.0 Index]