BbcSE: Constructor for BbcSE

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

BbcSE is a constructor for BbcSE.

Usage

BbcSE(
  counts = matrix(0, 0, 0),
  granges = rep(GRanges(seqnames = "foobar", ranges = 0:0), nrow(counts)),
  aln_metrics = matrix(0, 0, 0),
  ...
)

Arguments

counts	A count matrix with sample names as column names and gene names as row names.
granges	GRanges or GRangesList object. Optional.
aln_metrics	Matrix containing alignment metrics. Optional.
...	Passed to SummarizedExperiment constructor.

Details

If GRanges object is provided, the names must match the rownames of the counts matrix. The output object will show only the intersected genes between the the counts and the GRanges.

Value

A BbcSE object (extension of RangedSummarizedExperiment).

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.