read_moFF: Import a peptides summary file produced by moFF

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

Import a peptides summary file produced by moFF

Description

Imports a moFF (Argentini et al., 2016) .tab file and converts it into an MSnSet object (Gatto et al., 2012).

Usage

read_moFF(file, pattern = "sumIntensity_", remove_pattern = TRUE,
  shiny = FALSE, message = NULL)

Arguments

file	The name of a moFF .tab 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 "?????".
remove_pattern	A logical indicating whether the expression in "pattern" should be removed from the column names in the resulting MSnSet object. Defaults to FALSE.
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.

Argentini A, Goeminne LJE, Verheggen K, Hulstaert N, Staes A, Clement L & Martens L. moFF: a robust and automated approach to extract peptide ion intensities. Nature Methods. 2016 13:964–966. http://www.nature.com/nmeth/journal/v13/n12/full/nmeth.4075.html.

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