getStrandedCoverage: Get strand-specific coverage

In mdeber/BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Get strand-specific coverage

Description

Computes strand-specific coverage signal, and returns a GRanges object. Function also works for non-strand-specific data.

Usage

getStrandedCoverage(
  dataset.gr,
  field = "score",
  ncores = getOption("mc.cores", 2L)
)

Arguments

dataset.gr	A GRanges object either containing ranges for each read, or one in which readcounts for individual ranges are contained in metadata (typically in the "score" field). dataset.gr can also be a list of such GRanges objects.
field	The name of the metadata field that contains readcounts. If no metadata field contains readcounts, and each range represents a single read, set to NULL.
ncores	Number of cores to use for calculating coverage. For a single dataset, the max that will be used is 3, one for each possible strand (plus, minus, and unstranded). More cores can be used if dataset.gr is a list.

Value

A GRanges object with signal in the "score" metadata column. Note that the output is not automatically converted into a "basepair-resolution" GRanges object.

Author(s)

Mike DeBerardine

See Also

makeGRangesBRG, GenomicRanges::coverage

Examples

#--------------------------------------------------#
# Using included full-read data
#--------------------------------------------------#
# -> whole-read coverage sacrifices meaningful readcount
#    information, but can be useful for visualization,
#    e.g. for looking at RNA-seq data in a genome browser

data("PROseq_paired")

PROseq_paired[1:6]

getStrandedCoverage(PROseq_paired, ncores = 1)[1:6]

#--------------------------------------------------#
# Getting coverage from single bases of single reads
#--------------------------------------------------#

# included PROseq data is already single-base coverage
data("PROseq")
range(width(PROseq))

# undo coverage for the first 100 positions
ps <- PROseq[1:100]
ps_reads <- rep(ps, times = ps$score)
mcols(ps_reads) <- NULL

ps_reads[1:6]

# re-create coverage
getStrandedCoverage(ps_reads, field = NULL, ncores = 1)[1:6]

#--------------------------------------------------#
# Reversing makeGRangesBRG
#--------------------------------------------------#
# -> getStrandedCoverage doesn't return single-width
#    GRanges, which is useful because getting coverage
#    will merge adjacent bases with equivalent scores

# included PROseq data is already single-width
range(width(PROseq))
isDisjoint(PROseq)

ps_cov <- getStrandedCoverage(PROseq, ncores = 1)

range(width(ps_cov))
sum(score(PROseq)) == sum(score(ps_cov) * width(ps_cov))

# -> Look specifically at ranges that could be combined
neighbors <- c(shift(PROseq, 1), shift(PROseq, -1))
hits <- findOverlaps(PROseq, neighbors)
idx <- unique(from(hits)) # indices for PROseq with neighbor

PROseq[idx]

getStrandedCoverage(PROseq[idx], ncores = 1)

mdeber/BRGenomics documentation built on Aug. 3, 2024, 3:43 a.m.