import2MSnSet: Import a file in a prespecified format and convert it to an...

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

Import a file in a prespecified format and convert it to an MSnSet object

Description

Imports a file in MaxQuant (Cox and Mann, 2008), moFF (Argentini et al., 2016), mzTab (Griss et al., 2014) or Progenesis (Nonlinear Dynamics, Newcastle upon Tyne, U.K.) output format and converts it into an MSnSet object (Gatto et al., 2012). For custom import to an MSnSet object, please make use of the read2MSnSet function.

Usage

import2MSnSet(file, filetype, remove_pattern = NA,
  normalizedAbundances = TRUE, shiny = FALSE, message = NULL)

Arguments

file	The name of a file. For more details about how this argument can be specified, see read.table.
filetype	One of the following: "MaxQuant" for a MaxQuant peptides.txt file, "moFF" for a moFF .tab file, "mzTab" for an mzTab .tsv file or "Progenesis" for a Progenesis .csv file.
remove_pattern	A logical indicating whether the expression in "pattern" should be removed from the column names in the resulting MSnSet object. Defaults to NA, in which case the decision to remove the pattern is made depending on the filetype.
normalizedAbundances	A logical indicating whether normalized or raw abundances should be imported. This setting is only relevant for Progenesis data, where both types of data are available. Defaults to TRUE, in which case normalized data is imported.
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).
...	Further arguments that can be passed on to the read.table-like functions.

Details

When importing Progenesis data, import2MSnSet will automatically try to import normalized abundances. If that fails, import2MSnSet will try to import the raw abundances.

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.

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.

Griss J., Jones A.R., Sachsenberg T., Walzer M., Gatto L., Hartler J., Thallinger G.G., Salek R.M., Steinbeck C., Neuhauser N., Cox J., Neumann S., Fan J., Reisinger F., Xu Q.W., Del Toro N., Pérez-Riverol Y., Ghali F., Bandeira N., Xenarios I., Kohlbacher O., Vizcaíno J.A. & Hermjakob H.The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics. 2014 13(10):2765-75.

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