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:

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:

  1. sample_id_col (this can be repeated as row names)

  2. biological covariates

  3. 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]