# An R interface to the GMAP/GSNAP/GSTRUCT suite

## Documentation for package ‘gmapR’ version 1.42.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as.list-method | Class '"BamTallyParam"'
bamPaths-method | Class '"GsnapOutput"'
BamTallyParam | Class '"BamTallyParam"'
BamTallyParam-class | Class '"BamTallyParam"'
bam_tally | Per-position Alignment Summaries
bam_tally-method | Per-position Alignment Summaries
bam_tally-methods | Per-position Alignment Summaries
cmetindex | Call the cmetindex command
coerce-method | Class '"BamTallyParam"'
coerce-method | Class '"GmapGenome"'
directory | Get the Path to the Location on Disk from a gmapR Class
directory-method | Class '"GmapSnps"'
genome-method | Class '"GmapGenome"'
genome-method | Class '"GmapGenomeDirectory"'
genome-method | Per-position Alignment Summaries
getSeq-method | Class '"GmapGenome"'
GmapGenome | Class '"GmapGenome"'
GmapGenome-class | Class '"GmapGenome"'
GmapGenomeDirectory | Class '"GmapGenomeDirectory"'
GmapGenomeDirectory-class | Class '"GmapGenomeDirectory"'
GmapSnpDirectory | Class '"GmapSnpDirectory"'
GmapSnpDirectory-class | Class '"GmapSnpDirectory"'
GmapSnps | Class '"GmapSnps"'
GmapSnps-class | Class '"GmapSnps"'
gmap_build-method | Build Gmap/Gsnap Genome
gmap_build-methods | Build Gmap/Gsnap Genome
gsnap | Align a Set of Reads Using the GSNAP Aligner
gsnap-method | Align a Set of Reads Using the GSNAP Aligner
gsnap-methods | Align a Set of Reads Using the GSNAP Aligner
GsnapOutput | Class '"GsnapOutput"'
GsnapOutput-class | Class '"GsnapOutput"'
GsnapParam | Class '"GsnapParam"'
GsnapParam-class | Class '"GsnapParam"'
length-method | Class '"GmapSnpDirectory"'
makeGmapGenomePackage | Function to create a GmapGenome package from a GmapGenome object
names-method | Class '"GmapSnpDirectory"'
path-method | Class '"GmapGenome"'
path-method | Class '"GmapGenomeDirectory"'
path-method | Class '"GmapSnpDirectory"'
path-method | Class '"GsnapOutput"'
path-method | gmapR2 internals
seqinfo-method | Class '"GmapGenome"'
snps<- | Class '"GmapGenome"'
snps<--method | Class '"GmapGenome"'
snps<--method | Class '"GmapSnpDirectory"'
spliceSites<- | Class '"GmapGenome"'
spliceSites<--method | Class '"GmapGenome"'
TP53Genome | Demo genome around TP53
TP53Which | Demo genome around TP53
variantSummary | Per-position Alignment Summaries
[[<--method | Class '"GmapSnpDirectory"'