SpectroMinetoMSstatsTMTFormat {MSstatsTMT} | R Documentation

## 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)

[Package MSstatsTMT version 2.0.1 Index]