SpectronauttoMSstatsFormat {MSstats} | R Documentation |
Convert Spectronaut output into the required input format for MSstats.
SpectronauttoMSstatsFormat(input, annotation = NULL, intensity = 'PeakArea', filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01, useUniquePeptide = TRUE, fewMeasurements="remove", removeProtein_with1Feature = FALSE, summaryforMultipleRows=max)
input |
name of Spectronaut output, which is long-format. ProteinName, PeptideSequence, PrecursorCharge, FragmentIon, ProductCharge, IsotopeLabelType, Condition, BioReplicate, Run, Intensity, F.ExcludedFromQuantification are required. Rows with F.ExcludedFromQuantification=True will be removed. |
annotation |
name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Spectronaut, use annotation=NULL (default). It will use the annotation information from input. |
intensity |
'PeakArea'(default) uses not normalized peak area. 'NormalizedPeakArea' uses peak area normalized by Spectronaut. |
filter_with_Qvalue |
TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in EG.Qvalue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose. |
qvalue_cutoff |
Cutoff for EG.Qvalue. 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 feature, which is the combination of peptide, precursor charge, fragment 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)
# Please check section 5.2. # Suggested workflow with Spectronaut output for DIA in MSstats user manual. # Output of SpectronauttoMSstatsFormat function # should have the same 10 columns as an example dataset. head(DDARawData)