Filter features in a SummarizedExperiment object

Filter the features (rows) in a SummarizedExperiment object based on a user-defined combination of filters.

filterFeaturesSE(sce, filtersSE = list(), plotUpset = TRUE, exclFile = NULL)

Arguments

sce

A SummarizedExperiment object (or a derivative).

filtersSE

A named list, where each element is a function that takes a SummarizedExperiment object as input and returns a logical vector of the same length as the number of rows in sce, and where TRUE implies that the row should be retained. Default sets of filtering functions for input data from different tools are provided (see ?defaultFiltersSE).

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

# MaxQuant
sce <- importExperiment(inFile = system.file("extdata", "mq_example",
                                             "1356_proteinGroups.txt",
                                             package = "einprot"),
                        iColPattern = "^LFQ.intensity.")$sce

dim(sce)
#> [1] 463   9
sce <- filterFeaturesSE(sce = sce, filtersSE = einprotMQFilters,
                        plotUpset = TRUE)
#> 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] 231   9

# ProteomeDiscoverer, 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 <- filterFeaturesSE(sce = sce, filtersSE = einprotPDTMTProteinFilters,
                        plotUpset = TRUE)

dim(sce)
#> [1] 1087   16

# ProteomeDiscoverer, 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 <- filterFeaturesSE(sce = sce, filtersSE = einprotPDTMTPeptideGroupFilters)

dim(sce)
#> [1] 641  16

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

dim(sce)
#> [1] 453   9
sce <- filterFeaturesSE(sce = sce, filtersSE = einprotFragPipeFilters,
                       plotUpset = TRUE)

dim(sce)
#> [1] 355   9