get_spike_depth: get the (max, median, or mean) coverage for spike-in contigs...

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

get the (max, median, or mean) coverage for spike-in contigs from a BAM/CRAM

Description

get the (max, median, or mean) coverage for spike-in contigs from a BAM/CRAM

Usage

get_spike_depth(covg, spike_gr = NULL, spike = NULL, how = c("max", "mean"))

Arguments

covg	the coverage RleList
spike_gr	the spike-in GRanges (default: figure out from seqinfo)
spike	information about the spikes (default: load spike)
how	how to summarize the per-spike coverage (max)

Value

     a GRanges with summarized coverage and features for each

Examples

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

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

covg <- get_spiked_coverage(sb, bp=bp, gr=mgr)
get_spike_depth(covg, spike_gr=mgr, spike=spike)

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