├── .travis.yml ├── CandiHap.Rproj ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── AllClasses.R ├── AllGenerics.R ├── Function.R ├── data.R ├── genetrack.R ├── misc.R ├── plots.R └── zzz.R ├── README.md ├── _config.yml ├── data └── snp.rda └── man ├── GRangesInfo-class.Rd ├── OverlapInfo-class.Rd ├── SeqHap-class.Rd ├── aov.pheno.test.Rd ├── dot-GENE_TYPES.Rd ├── dot-check_same_or_not.Rd ├── dot-colnames.mcol.Rd ├── dot-detect_file.Rd ├── dot-getlist.Rd ├── dot-unlist.name.Rd ├── expandRange.Rd ├── findover.Rd ├── hapnet.Rd ├── importGFF.Rd ├── preGranges.Rd ├── read.data.Rd ├── read.hmp.Rd ├── read.pheno.Rd ├── read.vcf.Rd ├── read_data.Rd ├── read_hmp.Rd ├── read_pheno.Rd ├── read_vcf.Rd ├── results-SeqHap-method.Rd ├── results.Rd ├── seqs-SeqHap-method.Rd ├── seqs.Rd ├── snboxplot.Rd ├── snp.Rd ├── snp2fasta.Rd ├── snp2hap.Rd ├── snplot.Rd └── snptrack.Rd /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/.travis.yml -------------------------------------------------------------------------------- /CandiHap.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/CandiHap.Rproj -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/LICENSE -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/NAMESPACE -------------------------------------------------------------------------------- /R/AllClasses.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/AllClasses.R -------------------------------------------------------------------------------- /R/AllGenerics.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/AllGenerics.R -------------------------------------------------------------------------------- /R/Function.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/Function.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/data.R -------------------------------------------------------------------------------- /R/genetrack.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/genetrack.R -------------------------------------------------------------------------------- /R/misc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/misc.R -------------------------------------------------------------------------------- /R/plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/plots.R -------------------------------------------------------------------------------- /R/zzz.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/R/zzz.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/README.md -------------------------------------------------------------------------------- /_config.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/_config.yml -------------------------------------------------------------------------------- /data/snp.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/data/snp.rda -------------------------------------------------------------------------------- /man/GRangesInfo-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/GRangesInfo-class.Rd -------------------------------------------------------------------------------- /man/OverlapInfo-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/OverlapInfo-class.Rd -------------------------------------------------------------------------------- /man/SeqHap-class.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/SeqHap-class.Rd -------------------------------------------------------------------------------- /man/aov.pheno.test.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/aov.pheno.test.Rd -------------------------------------------------------------------------------- /man/dot-GENE_TYPES.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/dot-GENE_TYPES.Rd -------------------------------------------------------------------------------- /man/dot-check_same_or_not.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/dot-check_same_or_not.Rd -------------------------------------------------------------------------------- /man/dot-colnames.mcol.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/dot-colnames.mcol.Rd -------------------------------------------------------------------------------- /man/dot-detect_file.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/dot-detect_file.Rd -------------------------------------------------------------------------------- /man/dot-getlist.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/dot-getlist.Rd -------------------------------------------------------------------------------- /man/dot-unlist.name.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/dot-unlist.name.Rd -------------------------------------------------------------------------------- /man/expandRange.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/expandRange.Rd -------------------------------------------------------------------------------- /man/findover.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/findover.Rd -------------------------------------------------------------------------------- /man/hapnet.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/hapnet.Rd -------------------------------------------------------------------------------- /man/importGFF.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/importGFF.Rd -------------------------------------------------------------------------------- /man/preGranges.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/preGranges.Rd -------------------------------------------------------------------------------- /man/read.data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read.data.Rd -------------------------------------------------------------------------------- /man/read.hmp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read.hmp.Rd -------------------------------------------------------------------------------- /man/read.pheno.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read.pheno.Rd -------------------------------------------------------------------------------- /man/read.vcf.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read.vcf.Rd -------------------------------------------------------------------------------- /man/read_data.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read_data.Rd -------------------------------------------------------------------------------- /man/read_hmp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read_hmp.Rd -------------------------------------------------------------------------------- /man/read_pheno.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read_pheno.Rd -------------------------------------------------------------------------------- /man/read_vcf.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/read_vcf.Rd -------------------------------------------------------------------------------- /man/results-SeqHap-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/results-SeqHap-method.Rd -------------------------------------------------------------------------------- /man/results.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/results.Rd -------------------------------------------------------------------------------- /man/seqs-SeqHap-method.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/seqs-SeqHap-method.Rd -------------------------------------------------------------------------------- /man/seqs.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/seqs.Rd -------------------------------------------------------------------------------- /man/snboxplot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/snboxplot.Rd -------------------------------------------------------------------------------- /man/snp.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/snp.Rd -------------------------------------------------------------------------------- /man/snp2fasta.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/snp2fasta.Rd -------------------------------------------------------------------------------- /man/snp2hap.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/snp2hap.Rd -------------------------------------------------------------------------------- /man/snplot.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/snplot.Rd -------------------------------------------------------------------------------- /man/snptrack.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/guokai8/CandiHap/HEAD/man/snptrack.Rd --------------------------------------------------------------------------------