SkylinetoMSstatsLiPFormat {MSstatsLiP} | R Documentation |
Takes as as input both raw LiP and Trp outputs from Skyline.
SkylinetoMSstatsLiPFormat( LiP.data, TrP.data = NULL, annotation = NULL, removeiRT = TRUE, filter_with_Qvalue = TRUE, qvalue_cutoff = 0.01, useUniquePeptide = TRUE, removeFewMeasurements = TRUE, removeOxidationMpeptides = FALSE, removeProtein_with1Feature = FALSE, use_log_file = FALSE, append = FALSE, verbose = TRUE, log_file_path = NULL )
LiP.data |
name of LiP Skyline output, which is long-format. |
TrP.data |
name of TrP Skyline output, which is long-format. |
annotation |
name of 'annotation.txt' data which includes Condition, BioReplicate, Run. If annotation is already complete in Skyline, use annotation=NULL (default). It will use the annotation information from input. |
removeiRT |
TRUE (default) will remove the proteins or peptides which are labeld 'iRT' in 'StandardType' column. FALSE will keep them. |
filter_with_Qvalue |
TRUE(default) will filter out the intensities that have greater than qvalue_cutoff in DetectionQValue column. Those intensities will be replaced with zero and will be considered as censored missing values for imputation purpose. |
qvalue_cutoff |
Cutoff for DetectionQValue. 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. |
removeOxidationMpeptides |
TRUE will remove the peptides including 'oxidation (M)' in modification. FALSE is default. |
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. |
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 saved to a 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. |
a list
of two data.frames in MSstatsLiP
format
## Output will be in format head(MSstatsLiP_data[["LiP"]]) head(MSstatsLiP_data[["TrP"]])