center_peptide_batch_medians {proBatch}R Documentation

Median centering of the peptides (per batch median)

Description

Median centering of the peptides (per batch median)

Usage

center_peptide_batch_medians(df_long, sample_annotation = NULL,
  sample_id_col = "FullRunName", batch_col = "MS_batch",
  feature_id_col = "peptide_group_label", measure_col = "Intensity")

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)

sample_annotation

data frame with sample ID, technical (e.g. MS batches) and biological (e.g. Diet) covariates

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

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.

measure_col

if df_long is among the parameters, it is the column with expression/abundance/intensity, otherwise, it is used internally for consistency

Value

df_long-size long format data with batch-effect corrected with per-feature batch median centering in Intensity_normalized column

Examples

median_centered_proteome <- center_peptide_batch_medians(
example_proteome, example_sample_annotation)


[Package proBatch version 1.0.0 Index]