sequence-formats-1.5.1.3: A package with basic parsing utilities for several Bioinformatic data formats.

Index

Chrom 
1 (Type/Class)SequenceFormats.Utils
2 (Data Constructor)SequenceFormats.Utils
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
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
getDosagesSequenceFormats.VCF
getGenotypesSequenceFormats.VCF
HetSequenceFormats.Eigenstrat
HomAltSequenceFormats.Eigenstrat
HomRefSequenceFormats.Eigenstrat
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
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