Filter duplicate features

Keeps one feature from each set of duplicated features based on specified criteria, such as the feature with the highest values. Other duplicate features are removed.

filterDuplicateFeatures(
  se,
  mcol.name = "name",
  summary.stat = sum,
  selection.metric = max
)

Arguments

se

SummarizedExperiment

mcol.name

String specifying the colname for the experiment rowData

summary.stat

Function to summarize each feature (row) of the experiment

selection.metric

Function to select the row to keep when there are duplicate rows with the same mcol.name

Value

A SummarizedExperiment with duplicate features resolved.

Examples

library(SummarizedExperiment)
#> Loading required package: MatrixGenerics
#> Loading required package: matrixStats
#> 
#> Attaching package: ‘MatrixGenerics’
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
#>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
#>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
#>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
#>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
#>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
#>     colWeightedMeans, colWeightedMedians, colWeightedSds,
#>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
#>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
#>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
#>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
#>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
#>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
#>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
#>     rowWeightedSds, rowWeightedVars
#> Loading required package: GenomicRanges
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> Loading required package: generics
#> 
#> Attaching package: ‘generics’
#> The following objects are masked from ‘package:base’:
#> 
#>     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
#>     setequal, union
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
#>     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
#>     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
#>     unsplit, which.max, which.min
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following objects are masked from ‘package:Matrix’:
#> 
#>     expand, unname
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> Loading required package: IRanges
#> Loading required package: Seqinfo
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> Attaching package: ‘Biobase’
#> The following object is masked from ‘package:MatrixGenerics’:
#> 
#>     rowMedians
#> The following objects are masked from ‘package:matrixStats’:
#> 
#>     anyMissing, rowMedians

# Create a mock SummarizedExperiment with duplicates
counts <- matrix(1:10, ncol=2)
rdata <- DataFrame(name = c("GeneA", "GeneA", "GeneB", "GeneC", "GeneC"))
se <- SummarizedExperiment(assays=list(counts=counts), rowData=rdata)

# Filter duplicates, keeping the row with the max sum
se_filtered <- filterDuplicateFeatures(se, mcol.name="name", selection.metric=max)