Filter out features in FragPipe data

Exclude features with 'Combined.Total.Peptides' below minPeptides, or identified as either 'Reverse' (Protein name matching revPattern) or 'Potential.contaminant' (Protein name starting with contam_) by FragPipe.

filterFragPipe(
  sce,
  minPeptides,
  plotUpset = TRUE,
  revPattern = "^rev_",
  exclFile = NULL
)

Arguments

sce

A SummarizedExperiment object (or a derivative).

minPeptides

Numeric scalar, the minimum allowed value in the 'Combined.Total.Peptides' column in order to retain the feature.

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.

revPattern

Character scalar providing the pattern (a regular expression) used to identify decoys (reverse hits). The pattern is matched against the IDs in the FragPipe Protein column.

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

sce <- importExperiment(inFile = system.file("extdata", "fp_example",
                                             "combined_protein.tsv",
                                             package = "einprot"),
                        iColPattern = ".MaxLFQ.Intensity$")$sce

dim(sce)
#> [1] 453   9
sce <- filterFragPipe(sce = sce, minPeptides = 2,
                      plotUpset = TRUE,
                      revPattern = "^rev_")
#> Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
#> ℹ Please use `linewidth` instead.
#> ℹ The deprecated feature was likely used in the ComplexUpset package.
#>   Please report the issue at
#>   <https://github.com/krassowski/complex-upset/issues>.

dim(sce)
#> [1] 355   9