SpectronauttoMSstatsPTMFormat {MSstatsPTM} | R Documentation |
Takes as as input both raw PTM and global protein outputs from Spectronaut.
SpectronauttoMSstatsPTMFormat( PTM.data, fasta, Protein.data = NULL, annotation = NULL, intensity = "PeakArea", filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01, useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeProtein_with1Feature = FALSE, removeNonUniqueProteins = TRUE, modificationLabel = "Phospho", removeiRT = TRUE, summaryforMultipleRows = max, which.Conditions = "all" )
PTM.data |
name of PTM Spectronaut output, which is long-format. |
fasta |
A string of path to a FASTA file, used to match PTM peptides. |
Protein.data |
name of Global Protein Spectronaut output, which is long-format. |
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. |
removeFewMeasurements |
TRUE (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. |
removeNonUniqueProteins |
TRUE will remove proteins that were not uniquely identified. IE if the protein column contains multiple proteins seperated by ";". TRUE is default |
modificationLabel |
String of modification name. Default is 'Phospho'. |
removeiRT |
TRUE will remove proteins that contain iRT. True 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. |
which.Conditions |
list of conditions to format into MSstatsPTM format. If "all" all conditions will be used. Default is "all". |
a list of two data.tables named 'PTM' and 'PROTEIN' in the format required by MSstatsPTM.
# The output should be in the following format. head(raw.input$PTM) head(raw.input$PROTEIN)