API for Bioconductor-mirror/Rsamtools
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Global functions
ApplyPileupsParam Man page Source code
ApplyPileupsParam-class Man page
BamFile Man page Source code
BamFile-class Man page
BamFileList Man page Source code
BamFileList-class Man page
BamFile_guessIndex Source code
BamSampler Man page Source code
BamSampler-class Man page
BamViews Man page
BamViews,GRanges-method Man page
BamViews,missing-method Man page
BamViews-class Man page
BamViews_delegate Source code
BamViews_which Source code
BcfFile Man page Source code
BcfFile-class Man page
BcfFileList Man page Source code
BcfFileList-class Man page
FLAG_BITNAMES Man page
FaFile Man page Source code
FaFile-class Man page
FaFileList Man page Source code
FaFileList-class Man page
PileupFiles Man page Source code
PileupFiles,character-method Man page
PileupFiles,list-method Man page
PileupFiles-class Man page
PileupParam Man page Source code
PileupParam-class Man page
Rsamtools Man page
Rsamtools-package Man page
RsamtoolsFile Source code
RsamtoolsFile-class Man page
RsamtoolsFileList Man page
RsamtoolsFileList-class Man page
ScanBVcfParam-class Man page
ScanBamParam Man page
ScanBamParam,ANY-method Man page
ScanBamParam,GRanges-method Man page
ScanBamParam,RangesList-method Man page
ScanBamParam,missing-method Man page
ScanBamParam-class Man page
ScanBcfParam Man page Source code
ScanBcfParam,GRanges-method Man page
ScanBcfParam,GRangesList-method Man page
ScanBcfParam,RangesList-method Man page
ScanBcfParam,missing-method Man page
ScanBcfParam-class Man page
TabixFile Man page Source code
TabixFile-class Man page
TabixFileList Man page Source code
TabixFileList-class Man page
[,BamViews,ANY,ANY-method Man page
[,BamViews,ANY,missing-method Man page Man page
[,BamViews,missing,ANY-method Man page
applyPileups Man page
applyPileups,PileupFiles,ApplyPileupsParam-method Man page
applyPileups,PileupFiles,missing-method Man page
apply_bin_levels Source code
as.data.frame_list_of_lists Source code
as.factor_bin Source code
as.list_PileupParam Source code
asBam Man page
asBam,character-method Man page
asBcf Man page
asBcf,character-method Man page
asMates Man page
asMates,BamFile-method Man page
asMates,BamFileList-method Man page
asMates<- Man page
asMates<-,BamFile-method Man page
asMates<-,BamFileList-method Man page
asSam Man page
asSam,character-method Man page
ascii_offset Source code
bamDirname<- Man page
bamExperiment Man page Source code
bamFlag Man page Source code
bamFlag<- Man page
bamFlagAND Man page Source code
bamFlagAsBitMatrix Man page Source code
bamFlagTest Man page Source code
bamIndicies Man page Source code
bamMapqFilter Man page Source code
bamMapqFilter<- Man page
bamPaths Man page Source code
bamRanges Man page Source code
bamRanges<- Man page
bamReverseComplement Man page Source code
bamReverseComplement<- Man page
bamSamples Man page Source code
bamSamples<- Man page
bamSimpleCigar Man page Source code
bamSimpleCigar<- Man page
bamTag Man page Source code
bamTag<- Man page
bamTagFilter Man page Source code
bamTagFilter<- Man page
bamWhat Man page Source code
bamWhat<- Man page
bamWhich Man page Source code
bamWhich<- Man page
bamWhich<-,ScanBamParam,ANY-method Man page
bamWhich<-,ScanBamParam,GRanges-method Man page
bamWhich<-,ScanBamParam,RangesList-method Man page
bcfFixed Man page Source code
bcfGeno Man page Source code
bcfHeaderAsSimpleList Source code
bcfInfo Man page Source code
bcfMode Man page Source code
bcfSamples Man page Source code
bcfTrimEmpty Man page Source code
bcfWhich Man page Source code
bcf_template Source code
bgzip Man page Source code
bgzipTabix Man page Source code
bin_levels Source code
build_path Source code
bzfile-class Man page
calcBitPos Source code
checkPrefixSuffix Source code
check_qname_arg Source code
close.BamFile Man page Source code
close.BcfFile Source code
close.BcfFile Man page
close.FaFile Source code
close.FaFile Man page
close.PileupFiles Man page
close.RsamtoolsFileList Man page Source code
close.TabixFile Source code
close.TabixFile Man page
countBam Man page
countBam,BamFile-method Man page
countBam,BamFileList-method Man page
countBam,BamViews-method Man page
countBam,character-method Man page
countBam_postprocess Source code
countFa Man page
countFa,FaFile-method Man page
countFa,character-method Man page
countTabix Man page Source code
cycle_bins Man page
detailedSummary Source code
dim,BamViews-method Man page
dimnames,BamViews-method Man page
dimnames<-,BamViews,ANY-method Man page
dimnames<-,BamViews-method Man page
distinguish_nucleotides Man page
distinguish_strands Man page
extptr Source code
fifo-class Man page
file.rename Source code
filterBam Man page
filterBam,BamFile-method Man page
filterBam,character-method Man page
filterBam_FilterRules Source code
filterBam_preprocess Source code
findMateWithinGroups Source code
getSeq,FaFile-method Man page
getSeq,FaFileList-method Man page
gzfile-class Man page
has.wholenumbers Source code
hasUnmappedMate Man page
headerTabix Man page Source code
headerTabix,TabixFile-method Man page
headerTabix,character-method Man page
idxstatsBam Man page
idxstatsBam,BamFile-method Man page
idxstatsBam,character-method Man page
ignore_query_Ns Man page
include_deletions Man page
include_insertions Man page
index Man page
index,RsamtoolsFile-method Man page
index,RsamtoolsFileList-method Man page
index<- Man page
index<-,RsamtoolsFile-method Man page
index<-,RsamtoolsFileList-method Man page
indexBam Man page
indexBam,BamFile-method Man page
indexBam,character-method Man page
indexBcf Man page
indexBcf,BcfFile-method Man page
indexBcf,character-method Man page
indexFa Man page
indexFa,FaFile-method Man page
indexFa,character-method Man page
indexTabix Man page Source code
isDuplicate Man page
isFirstMateRead Man page
isIncomplete,BamFile-method Man page
isMateMinusStrand Man page
isMinusStrand Man page
isNotPassingQualityControls Man page
isNotPrimaryRead Man page
isOpen,BamFile-method Man page
isOpen,BcfFile-method Man page
isOpen,FaFile-method Man page
isOpen,PileupFiles-method Man page
isOpen,RsamtoolsFile-method Man page
isOpen,RsamtoolsFileList-method Man page
isOpen,TabixFile-method Man page
isPaired Man page
isProperPair Man page
isSecondMateRead Man page
isSecondaryAlignment Man page
isUnmappedQuery Man page
left_bins Man page
load_bamcols_from_scanBam_res Source code
make_unique Source code
max_depth Man page
mergeBam Man page
mergeBam,BamFileList-method Man page
mergeBam,character-method Man page
metacols_run_lengths Source code
min_base_quality Man page
min_mapq Man page
min_minor_allele_depth Man page
min_nucleotide_depth Man page
names,BamViews-method Man page
names,RsamtoolsFileList-method Man page
names<-,BamViews-method Man page
normalizePath Source code
normalizeRangesList Source code
normalize_tagFilter Source code
o_bam Source code
o_bcf Source code
o_check_exists Source code
obeyQname Man page
obeyQname,BamFile-method Man page
obeyQname,BamFileList-method Man page
obeyQname<- Man page
obeyQname<-,BamFile-method Man page
obeyQname<-,BamFileList-method Man page
onLoad Source code
open.BamFile Man page Source code
open.BcfFile Man page Source code
open.FaFile Man page Source code
open.PileupFiles Man page
open.RsamtoolsFileList Man page Source code
open.TabixFile Man page Source code
path Man page
path,RsamtoolsFile-method Man page
path,RsamtoolsFileList-method Man page
phred2ASCIIOffset Man page Source code
phred2ascii_char Source code
phred2ascii_int Source code
pileup Man page Source code
pileup,BamFile-method Man page
pileup,character-method Man page
pileupWhat Source code
pipe-class Man page
pkgLd Source code
pkgMk Source code
plpFiles Man page Source code
plpFlag Man page Source code
plpFlag<- Man page
plpMaxDepth Man page Source code
plpMaxDepth<- Man page
plpMinBaseQuality Man page Source code
plpMinBaseQuality<- Man page
plpMinDepth Man page Source code
plpMinDepth<- Man page
plpMinMapQuality Man page Source code
plpMinMapQuality<- Man page
plpParam Man page Source code
plpWhat Man page Source code
plpWhat<- Man page
plpWhich Man page Source code
plpWhich<- Man page
plpYieldAll Man page Source code
plpYieldAll<- Man page
plpYieldBy Man page Source code
plpYieldBy<- Man page
plpYieldSize Man page Source code
plpYieldSize<- Man page
ppath Source code
preprocess_bins Source code
printDetailedSummary Source code
printMainSummary Source code
printSummaryHeader Source code
printSummaryLine Source code
qnamePrefixEnd Man page
qnamePrefixEnd,BamFile-method Man page
qnamePrefixEnd,BamFileList-method Man page
qnamePrefixEnd<- Man page
qnamePrefixEnd<-,BamFile-method Man page
qnamePrefixEnd<-,BamFileList-method Man page
qnameSuffixStart Man page
qnameSuffixStart,BamFile-method Man page
qnameSuffixStart,BamFileList-method Man page
qnameSuffixStart<- Man page
qnameSuffixStart<-,BamFile-method Man page
qnameSuffixStart<-,BamFileList-method Man page
query_bins Man page
quickBamCounts Man page Source code
quickBamFlagSummary Man page
quickBamFlagSummary,BamFile-method Man page
quickBamFlagSummary,character-method Man page
quickBamFlagSummary,list-method Man page
quickCountBam Man page Source code
razip Man page Source code
readPileup Man page
readPileup,character-method Man page
readPileup,connection-method Man page
readPileup_SNP Source code
readPileup_indel Source code
readPileup_indel_idx Source code
readPileup_table Source code
runlen Source code
sValidHit Source code
scanBam Man page
scanBam,BamFile-method Man page
scanBam,BamSampler-method Man page
scanBam,BamViews-method Man page
scanBam,character-method Man page
scanBamFlag Man page Source code
scanBamHeader Man page
scanBamHeader,BamFile-method Man page
scanBamHeader,character-method Man page
scanBamTemplate Source code
scanBamWhat Man page Source code
scanBam_extract_which_labels Source code
scanBam_postprocess Source code
scanBam_template Source code
scanBcf Man page
scanBcf,BcfFile-method Man page
scanBcf,character-method Man page
scanBcfHeader Man page
scanBcfHeader,BcfFile-method Man page
scanBcfHeader,character-method Man page
scanFa Man page Source code
scanFa,FaFile,GRanges-method Man page
scanFa,FaFile,RangesList-method Man page
scanFa,FaFile,missing-method Man page
scanFa,character,GRanges-method Man page
scanFa,character,RangesList-method Man page
scanFa,character,missing-method Man page
scanFaIndex Man page
scanFaIndex,FaFile-method Man page
scanFaIndex,FaFileList-method Man page
scanFaIndex,character-method Man page
scanTabix Man page
scanTabix,TabixFile,GRanges-method Man page
scanTabix,TabixFile,RangesList-method Man page
scanTabix,TabixFile,missing-method Man page
scanTabix,character,ANY-method Man page
scanTabix,character,GRanges-method Man page
scanTabix,character,RangesList-method Man page
scanTabix,character,missing-method Man page
schemaBuilder Source code
seqinfo,BamFile-method Man page
seqinfo,BamFileList-method Man page
seqinfo,FaFile-method Man page
seqnamesTabix Man page Source code
seqnamesTabix,TabixFile-method Man page
seqnamesTabix,character-method Man page
show,ApplyPileupsParam-method Man page
show,BamFile-method Man page
show,BamFileList-method Man page
show,BamSampler-method Man page
show,BamViews-method Man page
show,PileupFiles-method Man page
show,PileupParam-method Man page
show,RsamtoolsFile-method Man page
show,ScanBVcfParam-method Man page
show,ScanBamParam-method Man page
show_classname Source code
sortBam Man page
sortBam,BamFile-method Man page
sortBam,character-method Man page
strandHelper Source code
tabix_scan Source code
testPairedEndBam Man page
testPairedEndBam,BamFile-method Man page
testPairedEndBam,character-method Man page
unz-class Man page
url-class Man page
uunlist Source code
yieldBam Man page
yieldSize Man page
yieldSize,RsamtoolsFile-method Man page
yieldSize,RsamtoolsFileList-method Man page
yieldSize<- Man page
yieldSize<-,RsamtoolsFile-method Man page
yieldSize<-,RsamtoolsFileList-method Man page
yieldTabix Man page
yieldTabix,TabixFile-method Man page
zip Source code
Bioconductor-mirror/Rsamtools documentation built on June 1, 2017, 1:10 a.m.