dpeaqms.csv2msms: Converts a csv style file into an MSMS data frame that can be...

In dpeaqms: Differential Protein Expression Analysis using Quantitative Mass Spectrometry Data (dpeaqms)

Description

This function will take a csv file and extract reporter ion intensity, MS/MS and protein accession information in order to create an MSMS data frame useable by the other functions in the dpeaqms package

Usage

  dpeaqms.csv2msms(csvfiles, proteinColumn, msmsidColumn,
                   reporterIonNames, sampleGroupAssignment,
                   includeUnknownProteins)

Arguments

csvfiles	The csvfile(s) containing the reporter ion intensities, protein accession and other ms/ms information. The default is NULL.
proteinColumn	The column number corresponding to the protein accession. The default is 1 i.e. the first column.
msmsidColumn	The column number(s) to use in order to construct the MS/MS identifier. The default is NULL in which case the msmsIDs will simple be integers.
reporterIonNames	A list containing the reporter ion intensity column names. By default these are those for a TMT 6-plex i.e. c(126,127,128,129,130,131)
sampleGroupAssignment	The groups to which the samples labeled with the above reporter ions are assigned. By default assumes a TMT 6-plex and assigns the first three to a CTL group and the second three to a TRT group i.e. c("CTL","CTL","CTL","TRT","TRT","TRT")

.

includeUnknownProteins

This is a boolean which controls whether (TRUE) or not (FALSE) MSMS spectra with no known protein accessions are assigned to "Unknown" protein accession. The default is TRUE.

dpeaqms documentation built on May 2, 2019, 4:46 p.m.