API for gmapR
An R interface to the GMAP/GSNAP/GSTRUCT suite

Global functions
..gmap Source code
..gsnap Source code
.atoiindex Source code
.bam_tally_C Source code
.cmetindex Source code
.commandLine Source code
.commandLine.handleMissingArgs Source code
.get_genome Source code
.gmap Source code
.gmapGenomeCreated Source code
.gmap_build Source code
.gsnap Source code
.iit_store Source code
.makeCdsIIT Source code
.make_iit_interval Source code
.normArgDb Source code
.snpindex Source code
.system Source code
.system_gsnap Source code
.test Source code
.valid_GmapOutput Source code
.valid_GsnapOutput Source code
.valid_GsnapParam Source code
.valid_GsnapParam_batch Source code
.valid_GsnapParam_format Source code
.valid_GsnapParam_max_mismatches Source code
.valid_GsnapParam_mode Source code
.valid_GsnapParam_nofails Source code
.valid_GsnapParam_novelsplicing Source code
.valid_GsnapParam_npaths Source code
.valid_GsnapParam_nthreads Source code
.valid_GsnapParam_part Source code
.valid_GsnapParam_quiet_if_excessive Source code
.valid_GsnapParam_read_group_id Source code
.valid_GsnapParam_read_group_name Source code
.valid_GsnapParam_splicing Source code
.valid_GsnapParam_split_output Source code
.valid_GsnapParam_suboptimal_levels Source code
.valid_GsnapParam_use_snps Source code
.valid_gmap_parameter Source code
BamTallyParam Man page Source code
BamTallyParam-class Man page
GeneGenome Source code
GmapAlignerParam_asList Source code
GmapBamReader Source code
GmapGenome Man page Source code
GmapGenome-class Man page
GmapGenomeDirectory Man page Source code
GmapGenomeDirectory-class Man page
GmapOutput Source code
GmapOutputList Source code
GmapParam Source code
GmapSnpDirectory Man page Source code
GmapSnpDirectory-class Man page
GmapSnps Man page Source code
GmapSnps-class Man page
GsnapOutput Man page Source code
GsnapOutput-class Man page
GsnapOutputList Source code
GsnapParam Man page Source code
GsnapParam-class Man page
IIT Source code
IITFile Source code
TP53Genome Man page Source code
TP53Which Man page Source code
TallyIIT Source code
[[<-,GmapSnpDirectory,ANY,ANY-method Man page
`gsnap_batch<-` Source code
`gsnap_extra<-` Source code
`gsnap_max_mismatches<-` Source code
`gsnap_mode<-` Source code
`gsnap_nofails<-` Source code
`gsnap_novelsplicing<-` Source code
`gsnap_npaths<-` Source code
`gsnap_nthreads<-` Source code
`gsnap_part<-` Source code
`gsnap_quiet_if_excessive<-` Source code
`gsnap_snpsdir<-` Source code
`gsnap_splicing<-` Source code
`gsnap_split_output<-` Source code
`gsnap_suboptimal_levels<-` Source code
`gsnap_use_snps<-` Source code
`iit<-` Source code
as.list,BamTallyParam-method Man page
as.list.GmapAlignerParam Source code
asSystemCall Source code
atoiindex Source code
bamFile Source code
bamPaths,GsnapOutput-method Man page
bam_tally Man page
bam_tally,BamFile-method Man page
bam_tally,GmapBamReader-method Man page
bam_tally,character-method Man page
bam_tally-methods Man page
checkPackageInstalled Source code
checkPackageVersion Source code
checkTallyConsistency Source code
close.IITFile Source code
cmetindex Man page Source code
coerce,BamTallyParam,list-method Man page
coerce,GmapGenome,DNAStringSet-method Man page
commandLine Source code
directory Man page Source code
directory,GmapSnps-method Man page
exonsOnTP53Genome Source code
fieldNames Source code
file_ext2 Source code
file_path_is_absolute Source code
file_path_is_dir Source code
formatToExt Source code
geneGenomeName Source code
geneOnTP53Genome Source code
genome,GmapGenome-method Man page
genome,GmapGenomeDirectory-method Man page
genome,TallyIIT-method Man page
getDefaultGmapGenomePath Source code
getDefaultGmapPath Source code
getExons Source code
getGeneRoi Source code
getSeq,GmapGenome-method Man page
gmapRange Source code
gmapVersion Source code
gmap_build,ANY,GmapGenome-method Man page
gmap_build,DNAStringSet,GmapGenome-method Man page
gmap_build,character,GmapGenome-method Man page
gmap_build-methods Man page
gsnap Man page
gsnap,character,character_OR_NULL,GsnapParam-method Man page
gsnap-methods Man page
gsnapInfo Source code
gsnapSucceeded Source code
gsnapVersion Source code
gsnap_batch Source code
gsnap_extra Source code
gsnap_max_mismatches Source code
gsnap_mode Source code
gsnap_nofails Source code
gsnap_novelsplicing Source code
gsnap_npaths Source code
gsnap_nthreads Source code
gsnap_part Source code
gsnap_quiet_if_excessive Source code
gsnap_snpsdir Source code
gsnap_splicing Source code
gsnap_split_output Source code
gsnap_suboptimal_levels Source code
gsnap_use_snps Source code
guessReadLengthFromBam Source code
iit Source code
is_dir Source code
length,GmapSnpDirectory-method Man page
makeGmapGenomePackage Man page Source code
mapsDirectory Source code
names,GmapSnpDirectory-method Man page
newGmapAlignerOutput Source code
newGmapAlignerParam Source code
normArgFields Source code
normArgSingleCharacterOrNULL Source code
normArgSingleInteger Source code
normArgSingleNumber Source code
normArgTRUEorFALSE Source code
normArgType Source code
normArgWhich Source code Source code
normalizeIndelAlleles Source code
open.IITFile Source code
openForWhich Source code
parseGsnapVersion Source code
path,GmapBamReader-method Man page
path,GmapGenome-method Man page
path,GmapGenomeDirectory-method Man page
path,GmapSnpDirectory-method Man page
path,GsnapOutput-method Man page
path,NULL-method Man page
paths Source code
samPaths Source code
seqinfo,GmapGenome-method Man page
showSlot Source code
showSlots Source code
snpindex Source code
snps<- Man page
snps<-,GmapGenome,ANY,ANY-method Man page
snps<-,GmapSnpDirectory,character,VCF-method Man page
snps<-,GmapSnpDirectory,character,character-method Man page
spliceSites<- Man page
spliceSites<-,GmapGenome,GRangesList-method Man page
spliceSites<-,GmapGenome,TxDb-method Man page
subsetRegion Source code
translateToP53Genome Source code
typeNames Source code
variantSummary Man page Source code
variantSummaryColumnDescriptions Source code
gmapR documentation built on April 29, 2020, 4:49 a.m.