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Filter transcripts in a `SummarizedExperiment` by minimum count/sample

Source: R/filter_se.R
filter_se.Rd

Subset a `SummarizedExperiment` to keep transcripts with more than `min_count` reads in strictly more than `min_samples` samples. The function updates assays, `rowData`, and relevant entries in `metadata()` (for example `readcounts` and `tx2gene`) so downstream helpers receive a consistent object.

Usage

filter_se(
  se,
  min_count = 5L,
  min_samples = 5L,
  assay_name = "counts",
  verbose = TRUE
)

Arguments

se

A `SummarizedExperiment` object containing transcript-level assays (rows = transcripts, columns = samples).

min_count

Integer threshold for per-sample counts (default 5L).

min_samples

Integer minimum number of samples exceeding `min_count` required to keep a transcript (default 5L).

assay_name

Name or index of the assay to use for filtering (default: 'counts'). If not present, the first assay is used.

verbose

Logical; print before/after counts when TRUE.

Value

A filtered `SummarizedExperiment`.

Examples

mat <- matrix(c(0, 6, 7, 2, 8, 9), nrow = 3, dimnames = list(paste0('tx', 1:3), paste0('S', 1:2)))
se <- SummarizedExperiment::SummarizedExperiment(assays = list(counts = mat))
filt <- filter_se(se, min_count = 5, min_samples = 1)
#> Transcripts: before = 3, after = 2
class(filt)
#> [1] "SummarizedExperiment"
#> attr(,"package")
#> [1] "SummarizedExperiment"