SpectroMinetoMSstatsTMTFormat: Import data from SpectroMine

In Vitek-Lab/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Import data from SpectroMine

Description

Import data from SpectroMine

Usage

SpectroMinetoMSstatsTMTFormat(
  input,
  annotation,
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum,
  use_log_file = TRUE,
  append = FALSE,
  verbose = TRUE,
  log_file_path = NULL,
  ...
)

Arguments

input	data name of SpectroMine PSM output. Read PSM sheet.
annotation	data frame which contains column Run, Fraction, TechRepMixture, Mixture, Channel, BioReplicate, Condition. Refer to the example 'annotation.mine' for the meaning of each column.
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 NA 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.
rmPSM_withfewMea_withinRun	TRUE (default) will remove the features that have 1 or 2 measurements within each Run.
rmProtein_with1Feature	TRUE will remove the proteins which have only 1 peptide and charge. Defaut is FALSE.
summaryforMultipleRows	sum(default) or max - when there are multiple measurements for certain feature in certain run, select the feature with the largest summation or maximal value.
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'.

Value

'data.frame' of class 'MSstatsTMT'

Examples

head(raw.mine)
head(annotation.mine)
input.mine <- SpectroMinetoMSstatsTMTFormat(raw.mine, annotation.mine)
head(input.mine)

Vitek-Lab/MSstatsTMT documentation built on Nov. 18, 2024, 11:30 a.m.