getSGFeatureCountsPerSample: Compatible fragment counts for splice graph features

Description Usage Arguments Value Author(s)

View source: R/counts.R

Description

Obtain counts of compatible fragments for splice graph features.

Usage

1
2
getSGFeatureCountsPerSample(features, file_bam, paired_end, sample_name,
  min_anchor, retain_coverage, verbose, cores)

Arguments

features

SGFeatures object

file_bam

BAM file with genomic RNA-seq read alignments

paired_end

Logical, TRUE for paired-end data, FALSE for single-end data

sample_name

Sample name used in messages

min_anchor

Integer specifiying minimum anchor length

retain_coverage

Logical indicating whether coverage for each exon should be retained as an RleList in metadata column “coverage”. This allows filtering of features using more stringent criteria after the initial prediction.

verbose

If TRUE, generate messages indicating progress

cores

Number of cores available for parallel processing

Value

Numeric vector of compatible fragment counts

Author(s)

Leonard Goldstein


Bioconductor-mirror/SGSeq documentation built on June 23, 2017, 4:25 p.m.