TENxFragments: Import fragments files from 10X

Usage

TENxFragments(resource, yieldSize = 200, which = GRanges(), ...)

Arguments

resource: character(1) The file path to the fragments resource, usually a compressed tabix file with extension .tsv.gz.
yieldSize: numeric() The number of records to read by default, 200 records will be imported. A warning will be emitted if not modified.
which: GRanges() A GRanges indicating the regions of interest. This get sent to RSamtools as the param input.
...: Further arguments to the class generator function (currently not used)

Value

A RaggedExperiment object class

Examples


fr <- system.file(
    "extdata", "pbmc_3k_atac_ex_fragments.tsv.gz",
    package = "TENxIO", mustWork = TRUE
)

tfr <- TENxFragments(fr)
#> Warning: Using default 'yieldSize' parameter

fra <- import(tfr)