get_spiked_coverage: tabulate coverage across assembly and spike contig subset in...

In trichelab/spiky: Spike-in calibration for cell-free MeDIP

tabulate coverage across assembly and spike contig subset in natural order

Description

FIXME: this is wicked slow, ask Herve if a faster version exists

Usage

get_spiked_coverage(bf, bp, gr)

Arguments

bf	the BamFile object
bp	the ScanBamParam object
gr	the GRanges with sorted seqlevels

Details

Refactored from scan_spiked_bam, this is a very simple wrapper

Value

a list of Rles

See Also

scan_spiked_bam

coverage

Examples

sb <- system.file("extdata", "example.spike.bam", package="spiky", 
                  mustWork=TRUE)
si <- seqinfo_from_header(sb) 
genome(si) <- "spike"
data(spike, package="spiky")
mgr <- get_merged_gr(si, spike=spike) # note canonicalized spikes

fl <- scanBamFlag(isDuplicate=FALSE, isPaired=TRUE, isProperPair=TRUE)
bp <- ScanBamParam(flag=fl)
bamMapqFilter(bp) <- 20
get_spiked_coverage(sb, bp=bp, gr=mgr)

trichelab/spiky documentation built on Sept. 17, 2022, 8:44 a.m.