rename_spike_seqlevels {spiky} | R Documentation

## 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

[Package spiky version 1.0.0 Index]