MaxQtoMSstatsFormat {MSstats} | R Documentation |
Import MaxQuant files
MaxQtoMSstatsFormat( evidence, annotation, proteinGroups, proteinID = "Proteins", useUniquePeptide = TRUE, summaryforMultipleRows = max, removeFewMeasurements = TRUE, removeMpeptides = FALSE, removeOxidationMpeptides = FALSE, removeProtein_with1Peptide = FALSE, use_log_file = TRUE, append = FALSE, verbose = TRUE, log_file_path = NULL, ... )
evidence |
name of 'evidence.txt' data, which includes feature-level data. |
annotation |
name of 'annotation.txt' data which includes Raw.file, Condition, BioReplicate, Run, IsotopeLabelType information. |
proteinGroups |
name of 'proteinGroups.txt' data. It needs to matching protein group ID. If proteinGroups=NULL, use 'Proteins' column in 'evidence.txt'. |
proteinID |
'Proteins'(default) or 'Leading.razor.protein' for Protein ID. |
useUniquePeptide |
TRUE (default) removes peptides that are assigned for more than one proteins. We assume to use unique peptide for each protein. |
summaryforMultipleRows |
max(default) or sum - when there are multiple measurements for certain feature and certain run, use highest or sum of multiple intensities. |
removeFewMeasurements |
TRUE (default) will remove the features that have 1 or 2 measurements across runs. |
removeMpeptides |
TRUE will remove the peptides including 'M' sequence. FALSE is default. |
removeOxidationMpeptides |
TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default. |
removeProtein_with1Peptide |
TRUE will remove the proteins which have only 1 peptide and charge. FALSE is default. |
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 wil 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 'append = TRUE', has to be a valid path to a file. |
... |
additional parameters to 'data.table::fread'. |
data.frame in the MSstats required format.
Warning: MSstats does not support for metabolic labeling or iTRAQ experiments.
Meena Choi, Olga Vitek.
mq_ev = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_ev.csv", package = "MSstatsConvert")) mq_pg = data.table::fread(system.file("tinytest/raw_data/MaxQuant/mq_pg.csv", package = "MSstatsConvert")) annot = data.table::fread(system.file("tinytest/raw_data/MaxQuant/annotation.csv", package = "MSstatsConvert")) maxq_imported = MaxQtoMSstatsFormat(mq_ev, annot, mq_pg, use_log_file = FALSE) head(maxq_imported)