sequence-formats-1.6.6.1: A package with basic parsing utilities for several Bioinformatic data formats.

Index

BedAheadSequenceFormats.Bed
BedBehindSequenceFormats.Bed
BedEntry 
1 (Type/Class)SequenceFormats.Bed
2 (Data Constructor)SequenceFormats.Bed
bedFileParserSequenceFormats.Bed
BedOnSequenceFormats.Bed
Chrom 
1 (Type/Class)SequenceFormats.Utils
2 (Data Constructor)SequenceFormats.Utils
chromFilterSequenceFormats.Genomic
consumeProducerSequenceFormats.Utils
EigenstratIndEntry 
1 (Type/Class)SequenceFormats.Eigenstrat
2 (Data Constructor)SequenceFormats.Eigenstrat
EigenstratSnpEntry 
1 (Type/Class)SequenceFormats.Eigenstrat
2 (Data Constructor)SequenceFormats.Eigenstrat
FemaleSequenceFormats.Eigenstrat
filterThroughBedSequenceFormats.Bed
ForwardStrandSequenceFormats.Pileup
FreqSumEntry 
1 (Type/Class)SequenceFormats.FreqSum
2 (Data Constructor)SequenceFormats.FreqSum
freqSumEntryToTextSequenceFormats.FreqSum
FreqSumHeader 
1 (Type/Class)SequenceFormats.FreqSum
2 (Data Constructor)SequenceFormats.FreqSum
fsAltSequenceFormats.FreqSum
fsChromSequenceFormats.FreqSum
fsCountsSequenceFormats.FreqSum
fsGeneticPosSequenceFormats.FreqSum
fshCountsSequenceFormats.FreqSum
fshNamesSequenceFormats.FreqSum
fsPosSequenceFormats.FreqSum
fsRefSequenceFormats.FreqSum
fsSnpIdSequenceFormats.FreqSum
GenoEntrySequenceFormats.Eigenstrat
GenoLineSequenceFormats.Eigenstrat
GenomicSequenceFormats.Genomic
genomicBaseSequenceFormats.Genomic
genomicChromSequenceFormats.Genomic
genomicFilterThroughBedSequenceFormats.Genomic
genomicPositionSequenceFormats.Genomic
getDosagesSequenceFormats.VCF
getGenotypesSequenceFormats.VCF
HetSequenceFormats.Eigenstrat
HomAltSequenceFormats.Eigenstrat
HomRefSequenceFormats.Eigenstrat
IntervalStatusSequenceFormats.Bed
isBiallelicSnpSequenceFormats.VCF
isTransversionSnpSequenceFormats.VCF
liftParsingErrorsSequenceFormats.Utils
loadFastaChromSequenceFormats.Fasta
MaleSequenceFormats.Eigenstrat
MissingSequenceFormats.Eigenstrat
pileupBasesSequenceFormats.Pileup
pileupChromSequenceFormats.Pileup
pileupPosSequenceFormats.Pileup
pileupRefSequenceFormats.Pileup
PileupRow 
1 (Type/Class)SequenceFormats.Pileup
2 (Data Constructor)SequenceFormats.Pileup
pileupStrandInfoSequenceFormats.Pileup
printFreqSumFileSequenceFormats.FreqSum
printFreqSumStdOutSequenceFormats.FreqSum
raConditionOnSequenceFormats.RareAlleleHistogram
raCountsSequenceFormats.RareAlleleHistogram
raExcludePatternsSequenceFormats.RareAlleleHistogram
raJackknifeEstimatesSequenceFormats.RareAlleleHistogram
raMaxAfSequenceFormats.RareAlleleHistogram
raMinAfSequenceFormats.RareAlleleHistogram
raNamesSequenceFormats.RareAlleleHistogram
raNVecSequenceFormats.RareAlleleHistogram
RareAlleleHistogram 
1 (Type/Class)SequenceFormats.RareAlleleHistogram
2 (Data Constructor)SequenceFormats.RareAlleleHistogram
raTotalNrSitesSequenceFormats.RareAlleleHistogram
readBedFileSequenceFormats.Bed
readBimFileSequenceFormats.Plink
readBimStdInSequenceFormats.Plink
readEigenstratSequenceFormats.Eigenstrat
readEigenstratIndSequenceFormats.Eigenstrat
readEigenstratSnpFileSequenceFormats.Eigenstrat
readEigenstratSnpStdInSequenceFormats.Eigenstrat
readFamFileSequenceFormats.Plink
readFileProdSequenceFormats.Utils
readFreqSumFileSequenceFormats.FreqSum
readFreqSumStdInSequenceFormats.FreqSum
readHistogramSequenceFormats.RareAlleleHistogram
readHistogramFromHandleSequenceFormats.RareAlleleHistogram
readNextFastaEntrySequenceFormats.Fasta
readPileupFromFileSequenceFormats.Pileup
readPileupFromStdInSequenceFormats.Pileup
readPlinkSequenceFormats.Plink
readPlinkBedFileSequenceFormats.Plink
readVCFfromFileSequenceFormats.VCF
readVCFfromProdSequenceFormats.VCF
readVCFfromStdInSequenceFormats.VCF
ReverseStrandSequenceFormats.Pileup
SeqFormatException 
1 (Type/Class)SequenceFormats.Utils
2 (Data Constructor)SequenceFormats.Utils
SexSequenceFormats.Eigenstrat
showSitePatternSequenceFormats.RareAlleleHistogram
SitePatternSequenceFormats.RareAlleleHistogram
snpAltSequenceFormats.Eigenstrat
snpChromSequenceFormats.Eigenstrat
snpGeneticPosSequenceFormats.Eigenstrat
snpIdSequenceFormats.Eigenstrat
snpPosSequenceFormats.Eigenstrat
snpRefSequenceFormats.Eigenstrat
StrandSequenceFormats.Pileup
unChromSequenceFormats.Utils
UnknownSequenceFormats.Eigenstrat
vcfAltSequenceFormats.VCF
vcfChromSequenceFormats.VCF
VCFentry 
1 (Type/Class)SequenceFormats.VCF
2 (Data Constructor)SequenceFormats.VCF
vcfFilterSequenceFormats.VCF
vcfFormatStringSequenceFormats.VCF
vcfGenotypeInfoSequenceFormats.VCF
VCFheader 
1 (Type/Class)SequenceFormats.VCF
2 (Data Constructor)SequenceFormats.VCF
vcfHeaderCommentsSequenceFormats.VCF
vcfIdSequenceFormats.VCF
vcfInfoSequenceFormats.VCF
vcfPosSequenceFormats.VCF
vcfQualSequenceFormats.VCF
vcfRefSequenceFormats.VCF
vcfSampleNamesSequenceFormats.VCF
vcfToFreqSumEntrySequenceFormats.VCF
wordSequenceFormats.Utils
writeBimSequenceFormats.Plink
writeEigenstratSequenceFormats.Eigenstrat
writeEigenstratGenoSequenceFormats.Eigenstrat
writeEigenstratIndFileSequenceFormats.Eigenstrat
writeEigenstratSnpSequenceFormats.Eigenstrat
writeHistogramFileSequenceFormats.RareAlleleHistogram
writeHistogramStdOutSequenceFormats.RareAlleleHistogram
writePlinkSequenceFormats.Plink