SkylinetoMSstatsFormat: Generate MSstats required input format for Skyline output

In lindsaypino/MSstats-patch: Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments

Description

Preprocess MSstats input report from Skyline and convert into the required input format for MSstats.

Usage

SkylinetoMSstatsFormat(input,
      annotation = NULL,
      removeiRT = TRUE,
      useUniquePeptide = TRUE,
      removeOxidationMpeptides = FALSE,
      removeProtein_with1Peptide = FALSE,
      filter_with_Qvalue = TRUE,
      qvalue_cutoff = 0.01)	

Arguments

input	name of MSstats input report from Skyline, which includes feature-level data.
annotation	name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input.
removeiRT	TRUE(default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them.
useUniquePeptide	TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein.
removeOxidationMpeptides	TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default.
removeProtein_with1Peptide	TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default.
filter_with_Qvalue	TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose.
qvalue_cutoff	Cutoff for DetectionQValue. default is 0.01.

Author(s)

Meena Choi, Olga Vitek.

Maintainer: Meena Choi ([e-mail])

lindsaypino/MSstats-patch documentation built on May 24, 2019, 6 p.m.