An R interface to the GMAP/GSNAP/GSTRUCT suite

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Documentation for package ‘gmapR’ version 1.48.0

• 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"'