get_merged_gr: get a GRanges of (by default, standard) chromosomes from...

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

get a GRanges of (by default, standard) chromosomes from seqinfo

Description

refactored from scan_spiked_bam to clarify information flow

Usage

get_merged_gr(si, spike, standard = TRUE)

Arguments

si	seqinfo, usually from a BAM/CRAM file with spike contigs
spike	database of spike-in standard sequence features (spike)
standard	trim to standard chromosomes? (TRUE)

Details

By default, get_merged_gr will return a GRanges with "standardized" genomic and spike contig names (i.e. genomic chr1-22, X, Y, M, and the canonical spike names in data(spike, package="spiky")).

The constraint to "standard" chromosomes on genomic contigs can be removed by setting standard to FALSE in the function arguments.

Value

     GRanges with two genomes: the organism assembly and "spike"

Examples

sb <- system.file("extdata", "example.spike.bam", package="spiky", 
                  mustWork=TRUE) 
si <- seqinfo_from_header(sb) 
genome(si) <- "spike" # no genomic contigs
data(spike, package="spiky")
get_merged_gr(si, spike=spike) # note canonicalized spikes

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