SkylinetoMSstatsFormat {MSstats} | R Documentation |
Preprocess MSstats input report from Skyline and convert into the required input format for MSstats.
SkylinetoMSstatsFormat(input, annotation = NULL, removeiRT = TRUE, filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01, useUniquePeptide = TRUE, fewMeasurements="remove", removeOxidationMpeptides = FALSE, removeProtein_with1Feature = FALSE)
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. |
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. |
useUniquePeptide |
TRUE(default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein. |
fewMeasurements |
'remove' (default) will remove the features that have 1 or 2 measurements across runs. |
removeOxidationMpeptides |
TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default. |
removeProtein_with1Feature |
TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default. |
data.frame with the required format of MSstats.
Meena Choi, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
# Please check section 4.2. Suggested workflow with Skyline output for DDA in MSstats user manual. # Output of SkylinetoMSstatsFormat function should have the same 10 columns as an example dataset. head(DDARawData)