SpectroMinetoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## Generate MSstatsTMT required input format for SpectroMine output

### Description

Convert SpectroMine output into the required input format for MSstatsTMT.

### Usage

    SpectroMinetoMSstatsTMTFormat(input, annotation, fraction = FALSE,
      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, Channel, Condition, BioReplicate, Mixture.
`fraction` | indicates whether the data has fractions. If there are fractions, then overlapped peptide ions will be removed and then fractions are combined for each mixture.
`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)

[Package MSstatsTMT version 1.1.2 Index]