SpectronauttoMSstatsLiPFormat: Converts raw LiP MS data from Spectronautt into the format...

In Vitek-Lab/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Converts raw LiP MS data from Spectronautt into the format needed for MSstatsLiP.

Description

Takes as as input both raw LiP and Trp outputs from Spectronautt.

Usage

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_"
)

Arguments

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 append = TRUE, has to be a valid path to a file.
base	start of the file name.

Value

a list of two data.frames in MSstatsLiP format

Examples

# 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"]])

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.