Filter out features in PD/TMT data

If inputLevel is "Proteins", exclude features with 'Score.Sequest.HT.Sequest.HT' below minScore, 'Number.of.Peptides' below minPeptides, or identified as 'Contaminant' by ProteomeDiscoverer. If inputLevel is "PeptideGroups", exclude features with 'Delta.Score.by.Search.Engine.Sequest.HT' below minDeltaScore, 'Number.of.PSMs' below minPSMs, or identified as 'Contaminant' by ProteomeDiscoverer.

filterPDTMT(
  sce,
  inputLevel,
  minScore = 0,
  minPeptides = 0,
  minDeltaScore = 0,
  minPSMs = 0,
  masterProteinsOnly = FALSE,
  modificationsCol = "Modifications",
  excludeUnmodifiedPeptides = FALSE,
  keepModifications = NULL,
  plotUpset = TRUE,
  exclFile = NULL
)

Arguments

sce

A SummarizedExperiment object (or a derivative).

inputLevel

Either "Proteins" or "PeptideGroups", indicating the type of features in sce.

minScore

Numeric scalar, the minimum allowed value in the 'Score.Sequest.HT.Sequest.HT' column in order to retain the feature. Only used if inputLevel is "Proteins".

minPeptides

Numeric scalar, the minimum allowed value in the 'Number.of.Peptides' column in order to retain the feature. Only used if inputLevel is "Proteins".

minDeltaScore

Numeric scalar, the minimum allowed value in the 'Delta.Score.by.Search.Engine.Sequest.HT' column in order to retain the feature. Only used if inputLevel is "PeptideGroups".

minPSMs

Numeric scalar, the minimum allowed value in the 'Number.of.PSMs' column in order to retain the feature. Only used if inputLevel is "PeptideGroups".

masterProteinsOnly

Logical scalar indicating whether only master proteins (where the Master column value is IsMasterProtein) should be retained.

modificationsCol

Character string pointing to a column containing modification details. excludeUnmodifiedPeptides and keepModifications will use information from this column. Only used if inputLevel is "PeptideGroups".

excludeUnmodifiedPeptides

Logical scalar, whether to filter out peptides without modifications. Only used if inputLevel is "PeptideGroups".

keepModifications

Character string (or NULL) indicating which modifications to retain in the analysis. Can be a regular expression, which will be matched against the modificationsCol. If NULL (the default), all rows are retained. Only used if inputLevel is "PeptideGroups".

plotUpset

Logical scalar, whether to generate an UpSet plot detailing the reasons for features being filtered out. Only generated if any feature is in fact filtered out.

exclFile

Character scalar, the path to a text file where the features that are filtered out are written. If NULL (default), excluded features are not recorded.

Value

A filtered object of the same type as sce.

Author

Charlotte Soneson

Examples

## Proteins
sce <- importExperiment(
    inFile = system.file("extdata", "pdtmt_example",
                         "Fig2_m23139_RTS_QC_varMods_Proteins.txt",
                         package = "einprot"),
    iColPattern = "^Abundance.F.+.Sample.")$sce

dim(sce)
#> [1] 1723   16
sce <- filterPDTMT(sce = sce, inputLevel = "Proteins", minScore = 2,
                   minPeptides = 2, plotUpset = TRUE)

dim(sce)
#> [1] 1087   16

## PeptideGroups
sce <- importExperiment(
    inFile = system.file("extdata", "pdtmt_example",
                         "Fig2_m23139_RTS_QC_varMods_PeptideGroups.txt",
                         package = "einprot"),
    iColPattern = "^Abundance.F.+.Sample.")$sce

dim(sce)
#> [1] 5756   16
sce <- filterPDTMT(sce = sce, inputLevel = "PeptideGroups",
                   minPSMs = 2, plotUpset = TRUE, minDeltaScore = 0.2,
                   modificationsCol = "Modifications.in.Master.Proteins",
                   excludeUnmodifiedPeptides = TRUE)

dim(sce)
#> [1] 641  16