readEvidenceFile: Read MaxQuant's evidence file

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Read MaxQuant's evidence file

Description

readEvidenceFile reads MaxQuant's evidence file. Contaminants and reverse sequences are filtered out.

Usage

readEvidenceFile(
  file,
  measure.cols = measureColumns,
  data.cols = evidenceColumns,
  zeroes.are.missing = TRUE
)

Arguments

file	File name.
measure.cols	Named list with measure columns to read.
data.cols	Named list with other columns to read (in addition to measure columns).
zeroes.are.missing	Logical. If TRUE zeroes are interpreted as missing data and replaced with NAs.

Details

There are two parameters controlling which columns are read from the evidence file. Parameter measure.cols selects columns with measurements: these are intensities (label-free, TMT) or ratios (SILAC). In the simplest case of label-free data, there is only one measure column: "Intensity". Parameter data.columns selects all other columns read from the evidence file. There are two default lists, supplied with the package, appropriate for an label-free experiment, measureColumns and evidenceColumns.

Value

Data frame with selected columns from the evidence file.

Examples

## Not run: 
library(proteusLabelFree)
evidenceFile <- system.file("extdata", "evidence.txt.gz", package="proteusLabelFree")
evi <- readEvidenceFile(evidenceFile)

## End(Not run)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.