read_MaxQuant: Import a MaxQuant peptides.txt file

In ludgergoeminne/MSqRob: Robust statistical inference for quantitative LC-MS proteomics

Import a MaxQuant peptides.txt file

Description

Imports a MaxQuant (Cox and Mann, 2008) peptides.txt file and converts it into an MSnSet object (Gatto et al., 2012).

Usage

read_MaxQuant(file, pattern = "Intensity ", remove_pattern = TRUE,
  shiny = FALSE, message = NULL)

Arguments

file	The name of a MaxQuant peptides.txt file. For more details about how this argument can be specified, see read.table.
pattern	A character string containing a regular expression that will be matched to the file's header. The columns matching the expression should be the columns containing the peptide intensity values. Defaults to "Intensity ".
remove_pattern	A logical indicating whether the expression in "pattern" should be removed from the column names in the resulting MSnSet object. Defaults to TRUE.
shiny	A logical indicating whether this function is being used by a Shiny app. Setting this to TRUE only works when using this function in a Shiny app and allows for dynamic progress bars. Defaults to FALSE.
message	Only used when shiny=TRUE. A single-element character vector: the message to be displayed to the user, or NULL to hide the current message (if any).

Value

An object of class MSnSet.

References

Gatto L, Lilley KS. MSnbase - an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics. 2012 Jan 15;28(2):288-9. https://doi.org/10.1093/bioinformatics/btr645.

Cox, J. and Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol, 2008, 26, pp 1367-72. http://www.nature.com/nbt/journal/v26/n12/full/nbt.1511.html.

ludgergoeminne/MSqRob documentation built on Jan. 11, 2023, 1:32 p.m.