SpectronauttoMSstatsLiPFormat {MSstatsLiP} | R Documentation |
Takes as as input both raw LiP and Trp outputs from Spectronautt.
SpectronauttoMSstatsLiPFormat( LiP.data, fasta, Trp.data = NULL, annotation = NULL, intensity = "PeakArea", filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01, useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeProtein_with1Feature = FALSE, removeNonUniqueProteins = TRUE, removeModifications = TRUE, removeiRT = TRUE, summaryforMultipleRows = max, which.Conditions = "all", use_log_file = FALSE, append = FALSE, verbose = TRUE, log_file_path = NULL, base = "MSstatsLiP_log_" )
LiP.data |
name of LiP Spectronaut output, which is long-format. |
fasta |
A string of path to a FASTA file, used to match LiP peptides. |
Trp.data |
name of TrP 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 |
removeModifications |
TRUE will remove peptide that contain a modification. Modification must be indicated by "[". TRUE is default |
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 MSstatsLiP format. If "all" all conditions will be used. Default is "all". |
use_log_file |
logical. If TRUE, information about data processing will be saved to a file. |
append |
logical. If TRUE, information about data processing will be added to an existing log file. |
verbose |
logical. If TRUE, information about data processing will be printed to the console. |
log_file_path |
character. Path to a file to which information about
data processing will be saved.
If not provided, such a file will be created automatically.
If |
base |
start of the file name. |
a list
of two data.frames
in MSstatsLiP format
# Output datasets of Spectronaut head(LiPRawData) head(TrPRawData) fasta_path <- system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP") MSstatsLiP_data <- SpectronauttoMSstatsLiPFormat(LiPRawData, fasta_path, TrPRawData) head(MSstatsLiP_data[["LiP"]]) head(MSstatsLiP_data[["TrP"]])