compute_coverage_long: Compute long-form coverage as a GRanges object

In sa-lee/superintronic: Tools for Working with Intron Signal

Description

Compute long-form coverage as a GRanges object

Usage

compute_coverage_long(
  spec,
  source,
  .which = NULL,
  .genome_info = NULL,
  .drop_empty = TRUE,
  .parallel = BiocParallel::bpparam()
)

## S4 method for signature 'character,missing'
compute_coverage_long(
  spec,
  source,
  .which = NULL,
  .genome_info = NULL,
  .drop_empty = TRUE,
  .parallel = BiocParallel::bpparam()
)

## S4 method for signature 'DataFrame,character'
compute_coverage_long(
  spec,
  source,
  .which = NULL,
  .genome_info = NULL,
  .drop_empty = TRUE,
  .parallel = BiocParallel::bpparam()
)

## S4 method for signature 'data.frame,character'
compute_coverage_long(
  spec,
  source,
  .which = NULL,
  .genome_info = NULL,
  .drop_empty = TRUE,
  .parallel = BiocParallel::bpparam()
)

Arguments

spec	a data.frame containing an experimental design
source	a column in the data identifying the name of BAM files
.which	an optional GRanges object (default = NULL) to compute coverage over a region (requires the BAM file to be indexed).
.genome_info	a GRanges object containing reference annotation (default = NULL)
.drop_empty	Filter ranges if they have zero coverage over an entire contig/chromosome (default TRUE)
.parallel	a BiocParallel object (default = BiocParallel::bpparam())

Details

This function computes coverage as a GRanges object, with a source column containing the name of the input BAM file(s), and a score column containing the coverage score.

The .genome_info argument takes a GRanges object containing contig/chromosome information. If supplied the resulting GRanges will be properly annotated with a seqinfo slot. This is important for ensure the integrity of any downstream overlap operations.

Value

a GRanges object

sa-lee/superintronic documentation built on Feb. 18, 2020, 10:36 a.m.