Infrastructure for Biostrings-based genome data packages and support for efficient SNP representation

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Documentation for package ‘BSgenome’ version 1.41.0

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A B C D E F G H I L M N O P R S U V W X misc

-- A --

alphabetFrequency-method BSgenomeViews objects
as.character-method BSgenomeViews objects
as.data.frame-method BSgenomeViews objects
as.list-method BSgenome objects
available.genomes Find available/installed genomes
available.SNPs SNP injection

-- B --

bsapply bsapply
BSgenome BSgenome objects
BSgenome-class BSgenome objects
BSgenome-utils BSgenome utilities
BSgenomeDataPkgSeed The BSgenomeForge functions
BSgenomeDataPkgSeed-class The BSgenomeForge functions
BSgenomeForge The BSgenomeForge functions
BSgenomeViews BSgenomeViews objects
BSgenomeViews-class BSgenomeViews objects
BSParams Class "BSParams"
BSParams-class Class "BSParams"

-- C --

class:BSgenome BSgenome objects
class:BSgenomeDataPkgSeed The BSgenomeForge functions
class:BSgenomeViews BSgenomeViews objects
class:BSParams Class "BSParams"
class:InjectSNPsHandler SNP injection
class:SNPlocs SNPlocs objects
class:XtraSNPlocs XtraSNPlocs objects
coerce-method BSgenomeViews objects
colnames-method XtraSNPlocs objects
commonName-method SNPlocs objects
commonName-method XtraSNPlocs objects
compatibleGenomes SNPlocs objects
compatibleGenomes-method SNPlocs objects
consensusMatrix-method BSgenomeViews objects
consensusString-method BSgenomeViews objects
countPWM-method BSgenome utilities

-- D --

dim-method XtraSNPlocs objects

-- E --

elementNROWS-method BSgenomeViews objects
end-method BSgenomeViews objects
export-method Export a BSgenome object as a FASTA or twoBit file
export-methods Export a BSgenome object as a FASTA or twoBit file
extractROWS-method BSgenomeViews objects

-- F --

forgeBSgenomeDataPkg The BSgenomeForge functions
forgeBSgenomeDataPkg-method The BSgenomeForge functions
forgeMasksFiles The BSgenomeForge functions
forgeSeqFiles The BSgenomeForge functions
forgeSeqlengthsFile The BSgenomeForge functions

-- G --

getBSgenome Find available/installed genomes
getListElement-method BSgenomeViews objects
getSeq-method getSeq method for BSgenome and XStringSet objects
granges-method BSgenomeViews objects

-- H --

hasOnlyBaseLetters-method BSgenomeViews objects

-- I --

injectSNPs SNP injection
injectSNPs-method SNP injection
InjectSNPsHandler SNP injection
InjectSNPsHandler-class SNP injection
installed.genomes Find available/installed genomes
installed.SNPs SNP injection

-- L --

length-method BSgenome objects
length-method BSgenomeViews objects
letterFrequency-method BSgenomeViews objects

-- M --

masknames BSgenome objects
masknames-method BSgenome objects
matchPWM-method BSgenome utilities
mseqnames BSgenome objects
mseqnames-method BSgenome objects

-- N --

names-method BSgenome objects
names-method BSgenomeViews objects
nchar-method BSgenomeViews objects
newSNPlocs SNPlocs objects
newXtraSNPlocs XtraSNPlocs objects
nucleotideFrequencyAt-method BSgenomeViews objects

-- O --

oligonucleotideFrequency-method BSgenomeViews objects
organism-method SNPlocs objects
organism-method XtraSNPlocs objects

-- P --

provider-method SNPlocs objects
provider-method XtraSNPlocs objects
providerVersion-method SNPlocs objects
providerVersion-method XtraSNPlocs objects

-- R --

ranges-method BSgenomeViews objects
referenceGenome SNPlocs objects
referenceGenome-method SNPlocs objects
referenceGenome-method XtraSNPlocs objects
releaseDate-method SNPlocs objects
releaseDate-method XtraSNPlocs objects
releaseName-method SNPlocs objects
releaseName-method XtraSNPlocs objects

-- S --

seqinfo-method BSgenome objects
seqinfo-method BSgenomeViews objects
seqinfo-method SNPlocs objects
seqinfo-method XtraSNPlocs objects
seqinfo<--method BSgenome objects
seqnames-method BSgenomeViews objects
seqnames-method SNPlocs objects
seqnames-method XtraSNPlocs objects
seqnames<--method BSgenome objects
seqtype-method BSgenomeViews objects
show-method BSgenome objects
show-method BSgenomeViews objects
show-method SNPlocs objects
show-method XtraSNPlocs objects
SNPcount SNP injection
snpcount SNPlocs objects
SNPcount-method SNP injection
snpcount-method SNPlocs objects
snpcount-method XtraSNPlocs objects
snpcount-method SNP injection
snpid2alleles SNPlocs objects
snpid2alleles-method SNPlocs objects
snpid2grange SNPlocs objects
snpid2grange-method SNPlocs objects
snpid2loc SNPlocs objects
snpid2loc-method SNPlocs objects
SNPlocs SNPlocs objects
snplocs SNPlocs objects
SNPlocs-class SNPlocs objects
SNPlocs-method SNP injection
snplocs-method SNPlocs objects
snplocs-method SNP injection
SNPlocs_pkgname SNP injection
SNPlocs_pkgname-method SNP injection
snpsById SNPlocs objects
snpsById-method SNPlocs objects
snpsById-method XtraSNPlocs objects
snpsByOverlaps SNPlocs objects
snpsByOverlaps-method SNPlocs objects
snpsByOverlaps-method XtraSNPlocs objects
snpsBySeqname SNPlocs objects
snpsBySeqname-method SNPlocs objects
snpsBySeqname-method XtraSNPlocs objects
sourceUrl BSgenome objects
sourceUrl-method BSgenome objects
species-method SNPlocs objects
species-method XtraSNPlocs objects
start-method BSgenomeViews objects
strand-method BSgenomeViews objects
subject-method BSgenomeViews objects

-- U --

uniqueLetters-method BSgenomeViews objects
unlist-method BSgenomeViews objects

-- V --

vcountPattern-method BSgenome utilities
vcountPDict-method BSgenome utilities
Views-method BSgenomeViews objects
vmatchPattern-method BSgenome utilities
vmatchPDict-method BSgenome utilities

-- W --

width-method BSgenomeViews objects
writeBSgenomeToFasta Export a BSgenome object as a FASTA or twoBit file
writeBSgenomeToTwobit Export a BSgenome object as a FASTA or twoBit file

-- X --

XtraSNPlocs XtraSNPlocs objects
XtraSNPlocs-class XtraSNPlocs objects

-- misc --

$-method BSgenome objects
[[-method BSgenome objects