Man pages for guokai8/CandiHap
Build Haplotye and Generate Figures
| aov.pheno.test | anova test for phenotype based on haplotype |
| dot-check_same_or_not | check if REF same as hap |
| dot-colnames.mcol | change mcols data colnames |
| dot-detect_file | detect file format for import gff or gff3 file modified based... |
| dot-GENE_TYPES | copy from GenomicFeatures |
| dot-getlist | get name of list |
| dot-unlist.name | unlist and add names |
| expandRange | expand range from start and end |
| findover | find overlap between target genes and hmp |
| GRangesInfo-class | Class "GRangesInfo" This class represents the extract gene... |
| hapnet | plot haplotype with network |
| importGFF | read GFF file into Granges object |
| OverlapInfo-class | Class "OverlapInfo" This class represents the extract gene... |
| preGranges | filter GRanges and add flanking regions |
| read_data | prepare GWAS data |
| read.data | prepare GWAS data |
| read_hmp | read hmp files and combine snp together |
| read.hmp | read hmp files and combine snp together |
| read_pheno | read hmp files and combine snp together |
| read.pheno | read hmp files and combine snp together |
| read_vcf | read vcf files |
| read.vcf | read vcf files |
| results | extract sequence form SeqHap object |
| results-SeqHap-method | extract final results from SeqHap object |
| SeqHap-class | Class "SeqHap" This class represents the result of overlap... |
| seqs | extract sequence form SeqHap object |
| seqs-SeqHap-method | extract sequence form SeqHap object |
| snboxplot | boxplot for haplotype testing based on phenotype |
| snp | snp |
| snp2fasta | snp data frame to vector |
| snp2hap | extract fasta from genotype file and find haplotype |
| snplot | plot snp with gene |
| snptrack | plot Gene Track with SNP information |
