rename_spike_seqlevels: for spike-in contigs in GRanges, match to standardized spike...

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

for spike-in contigs in GRanges, match to standardized spike seqlevels

Description

This function is essentially the opposite of rename_spikes, except that it works well on GRanges/GAlignments from or for merged genome+spike BAMs. If spike contigs are found, it will assign genome='spike' to those, while changing the seqlevels to standardized names that match rownames(spike).

Usage

rename_spike_seqlevels(x, spike = NULL)

Arguments

x	something with seqlevels (GRanges, GAlignments, Seqinfo...)
spike	a DataFrame where spike$sequence is a DNAStringSet (or NULL)

Value

     x, but with standardized spike seqlevels and genomes

See Also

    rename_spikes

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