readMaxQuantPeptides: Reading MaxQuant Output

In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

Description

Reads in "peptides.txt" output (or its compressed version) as MSnSet.

Usage

readMaxQuantPeptides(path = ".", msms_id_only = FALSE, verbose = 1)

Arguments

path	character path to the folder containing "peptides.txt file". It should be in "raw files folder/combined/txt" of MaxQuant output.
msms_id_only	logical If TRUE retains values associated with MS/MS peptide identifications only. Otherwise reports IDs identified both by MS/MS and match between the runs (MBR). Default it FALSE - that is reporting data from both type of identifications.
verbose	numeric controls the text output

Value

MSnSet object

Note

The "peptides.txt" file can be compressed (gzip) to save space.

The quantitative data reported by this function is in "Intensity" columns of the "peptides.txt" file.

Examples

# label-free data
m <- readMaxQuantPeptides(system.file("extdata/MaxQuantPep",
                                       package="vp.misc"))
exprs(m) <- log2(exprs(m))
exprs(m) <- sweep(exprs(m), 1, rowMeans(exprs(m), na.rm=TRUE), '-')
image_msnset(m)

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.