SpectroMinetoMSstatsTMTFormat: Generate MSstatsTMT required input format for SpectroMine...

In huang704/MSstatsTMT: Protein Significance Analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling

Description

Convert SpectroMine output into the required input format for MSstatsTMT.

Usage

SpectroMinetoMSstatsTMTFormat(
  input,
  annotation,
  filter_with_Qvalue = TRUE,
  qvalue_cutoff = 0.01,
  useUniquePeptide = TRUE,
  rmPSM_withMissing_withinRun = FALSE,
  rmPSM_withfewMea_withinRun = TRUE,
  rmProtein_with1Feature = FALSE,
  summaryforMultipleRows = sum
)

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_withMissing_withinRun	TRUE will remove PSM with any missing value within each Run. Defaut is FALSE.
rmPSM_withfewMea_withinRun	only for rmPSM_withMissing_withinRun = FALSE. 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.

Value

input for proteinSummarization function

Examples

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

huang704/MSstatsTMT documentation built on Jan. 1, 2021, 3:21 a.m.