sequence-formats-1.6.1: A package with basic parsing utilities for several Bioinformatic data formats.
Contents
Index
Index
Chrom
1 (Type/Class)
SequenceFormats.Utils
2 (Data Constructor)
SequenceFormats.Utils
consumeProducer
SequenceFormats.Utils
EigenstratIndEntry
1 (Type/Class)
SequenceFormats.Eigenstrat
2 (Data Constructor)
SequenceFormats.Eigenstrat
EigenstratSnpEntry
1 (Type/Class)
SequenceFormats.Eigenstrat
2 (Data Constructor)
SequenceFormats.Eigenstrat
Female
SequenceFormats.Eigenstrat
ForwardStrand
SequenceFormats.Pileup
FreqSumEntry
1 (Type/Class)
SequenceFormats.FreqSum
2 (Data Constructor)
SequenceFormats.FreqSum
freqSumEntryToText
SequenceFormats.FreqSum
FreqSumHeader
1 (Type/Class)
SequenceFormats.FreqSum
2 (Data Constructor)
SequenceFormats.FreqSum
fsAlt
SequenceFormats.FreqSum
fsChrom
SequenceFormats.FreqSum
fsCounts
SequenceFormats.FreqSum
fsGeneticPos
SequenceFormats.FreqSum
fshCounts
SequenceFormats.FreqSum
fshNames
SequenceFormats.FreqSum
fsPos
SequenceFormats.FreqSum
fsRef
SequenceFormats.FreqSum
fsSnpId
SequenceFormats.FreqSum
GenoEntry
SequenceFormats.Eigenstrat
GenoLine
SequenceFormats.Eigenstrat
getDosages
SequenceFormats.VCF
getGenotypes
SequenceFormats.VCF
Het
SequenceFormats.Eigenstrat
HomAlt
SequenceFormats.Eigenstrat
HomRef
SequenceFormats.Eigenstrat
isBiallelicSnp
SequenceFormats.VCF
isTransversionSnp
SequenceFormats.VCF
liftParsingErrors
SequenceFormats.Utils
loadFastaChrom
SequenceFormats.Fasta
Male
SequenceFormats.Eigenstrat
Missing
SequenceFormats.Eigenstrat
pileupBases
SequenceFormats.Pileup
pileupChrom
SequenceFormats.Pileup
pileupPos
SequenceFormats.Pileup
pileupRef
SequenceFormats.Pileup
PileupRow
1 (Type/Class)
SequenceFormats.Pileup
2 (Data Constructor)
SequenceFormats.Pileup
pileupStrandInfo
SequenceFormats.Pileup
printFreqSumFile
SequenceFormats.FreqSum
printFreqSumStdOut
SequenceFormats.FreqSum
raConditionOn
SequenceFormats.RareAlleleHistogram
raCounts
SequenceFormats.RareAlleleHistogram
raExcludePatterns
SequenceFormats.RareAlleleHistogram
raJackknifeEstimates
SequenceFormats.RareAlleleHistogram
raMaxAf
SequenceFormats.RareAlleleHistogram
raMinAf
SequenceFormats.RareAlleleHistogram
raNames
SequenceFormats.RareAlleleHistogram
raNVec
SequenceFormats.RareAlleleHistogram
RareAlleleHistogram
1 (Type/Class)
SequenceFormats.RareAlleleHistogram
2 (Data Constructor)
SequenceFormats.RareAlleleHistogram
raTotalNrSites
SequenceFormats.RareAlleleHistogram
readBimFile
SequenceFormats.Plink
readBimStdIn
SequenceFormats.Plink
readEigenstrat
SequenceFormats.Eigenstrat
readEigenstratInd
SequenceFormats.Eigenstrat
readEigenstratSnpFile
SequenceFormats.Eigenstrat
readEigenstratSnpStdIn
SequenceFormats.Eigenstrat
readFamFile
SequenceFormats.Plink
readFileProd
SequenceFormats.Utils
readFreqSumFile
SequenceFormats.FreqSum
readFreqSumStdIn
SequenceFormats.FreqSum
readHistogram
SequenceFormats.RareAlleleHistogram
readHistogramFromHandle
SequenceFormats.RareAlleleHistogram
readNextFastaEntry
SequenceFormats.Fasta
readPileupFromFile
SequenceFormats.Pileup
readPileupFromStdIn
SequenceFormats.Pileup
readPlink
SequenceFormats.Plink
readPlinkBedFile
SequenceFormats.Plink
readVCFfromFile
SequenceFormats.VCF
readVCFfromProd
SequenceFormats.VCF
readVCFfromStdIn
SequenceFormats.VCF
ReverseStrand
SequenceFormats.Pileup
SeqFormatException
1 (Type/Class)
SequenceFormats.Utils
2 (Data Constructor)
SequenceFormats.Utils
Sex
SequenceFormats.Eigenstrat
showSitePattern
SequenceFormats.RareAlleleHistogram
SitePattern
SequenceFormats.RareAlleleHistogram
snpAlt
SequenceFormats.Eigenstrat
snpChrom
SequenceFormats.Eigenstrat
snpGeneticPos
SequenceFormats.Eigenstrat
snpId
SequenceFormats.Eigenstrat
snpPos
SequenceFormats.Eigenstrat
snpRef
SequenceFormats.Eigenstrat
Strand
SequenceFormats.Pileup
unChrom
SequenceFormats.Utils
Unknown
SequenceFormats.Eigenstrat
vcfAlt
SequenceFormats.VCF
vcfChrom
SequenceFormats.VCF
VCFentry
1 (Type/Class)
SequenceFormats.VCF
2 (Data Constructor)
SequenceFormats.VCF
vcfFilter
SequenceFormats.VCF
vcfFormatString
SequenceFormats.VCF
vcfGenotypeInfo
SequenceFormats.VCF
VCFheader
1 (Type/Class)
SequenceFormats.VCF
2 (Data Constructor)
SequenceFormats.VCF
vcfHeaderComments
SequenceFormats.VCF
vcfId
SequenceFormats.VCF
vcfInfo
SequenceFormats.VCF
vcfPos
SequenceFormats.VCF
vcfQual
SequenceFormats.VCF
vcfRef
SequenceFormats.VCF
vcfSampleNames
SequenceFormats.VCF
vcfToFreqSumEntry
SequenceFormats.VCF
word
SequenceFormats.Utils
writeBim
SequenceFormats.Plink
writeEigenstrat
SequenceFormats.Eigenstrat
writeEigenstratGeno
SequenceFormats.Eigenstrat
writeEigenstratIndFile
SequenceFormats.Eigenstrat
writeEigenstratSnp
SequenceFormats.Eigenstrat
writeHistogramFile
SequenceFormats.RareAlleleHistogram
writeHistogramStdOut
SequenceFormats.RareAlleleHistogram
writePlink
SequenceFormats.Plink