cmetindex: Call the cmetindex command

In gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite

Description

Call the GMAP cmetindex command to build an index suitable for alignment of bisulfite-treated DNA, by allowing for C->T and G->A differences.

Usage

cmetindex(db, use_snps = NULL)

Arguments

db	The GmapGenome object
use_snps	A GmapSnps object for generating a SNP-tolerant index

Author(s)

Michael Lawrence

Examples

## Not run: 
    library(BSgenome.Dmelanogaster.UCSC.dm3)
    flyGG <- GmapGenome(Dmelanogaster, create = TRUE)
    cmetindex(flyGG)

## End(Not run)

gmapR documentation built on Nov. 8, 2020, 5:29 p.m.