View source: R/get_merged_gr.R
refactored from scan_spiked_bam to clarify information flow
get_merged_gr(si, spike, standard = TRUE)
seqinfo, usually from a BAM/CRAM file with spike contigs
database of spike-in standard sequence features (spike)
trim to standard chromosomes? (TRUE)
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.
GRanges with two genomes: the organism assembly and "spike"
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
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