OpenSWATHtoMSstatsFormat {MSstats} | R Documentation |
Preprocess MSstats input report from OpenSWATH and convert into the required input format for MSstats.
OpenSWATHtoMSstatsFormat(input, annotation = NULL, filter_with_mscore = TRUE, mscore_cutoff = 0.01, useUniquePeptide = TRUE, fewMeasurements="remove", removeProtein_with1Feature = FALSE, summaryforMultipleRows=max)
input |
name of MSstats input report from OpenSWATH, which includes feature-level data. |
annotation |
name of 'annotation.txt' data which includes Condition, BioReplicate, Run. Run should be the same as filename. |
filter_with_mscore |
TRUE(default) will filter out the features that have greater than mscore_cutoff in m_score column. Those features will be removed. |
mscore_cutoff |
Cutoff for m_score. 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. |
removeProtein_with1Feature |
TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default. |
summaryforMultipleRows |
max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities. |
data.frame with the required format of MSstats.
Meena Choi, Olga Vitek.
Maintainer: Meena Choi (mnchoi67@gmail.com)
# Example will be ready in next version.