AccINFO |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
addINFO |
Add Infomation to Haplotype Results |
addPromoter |
add promoter to annotation |
as.haplotype |
as.haplotype |
ashaplotype |
as.haplotype |
china |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
compareAllSites |
sites comparison |
DataSet |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
displayVarOnGeneModel |
Display Variants on Gene Model |
filterLargeP.link |
Pre-process of Large VCF File(s) |
filterLargep.link |
Pre-process of Large VCF File(s) |
filterLargeVCF |
Pre-process of Large VCF File(s) |
filter_hap |
Filter hap |
filter_hmp |
filter variants in hapmap format |
filter_plink.pedmap |
filter_plink.pedmap |
filter_table |
filter variants stored in table |
filter_vcf |
Filter VCF |
getGenePOS |
Get Gene Position |
getGeneRanges |
Get Gene Ranges |
getHapGroup |
Generate Haplotype Net Relationshop with Haplotype Result |
get_hapNet |
Generate Haplotype Net Relationshop with Haplotype Result |
gff |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
gffSetATGas0 |
Set Position of ATG as Zero |
gt.geno |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
hap2hmp |
Convert hapResult object to hapmap (hmp) format, for interact with other packages |
hapDistribution |
Display of Geography Distribution |
hapResult |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
hapSetATGas0 |
Set Position of ATG as Zero |
hapVsPheno |
hapVsPheno |
hapVsPhenoPerSite |
hapVsPhenoPerSite |
hapVsPhenos |
hapVsPhenos |
hap_summary |
Summary Hap Results |
hmp2hap |
Convert hapResult object to hapmap (hmp) format, for interact with other packages |
import_AccINFO |
Import Accession Information from File |
import_bed |
import annotation files in BED format |
import_gff |
Import Annotations from GFF Format File |
import_hap |
Import hapResult/hapSummary |
import_MultipleAlignment |
Import MultipleAlignment Result |
import_plink.pedmap |
import_plink.pedmap |
import_seqs |
Import Sequences |
import_vcf |
Import VCF from File |
LDheatmap |
This function produces a pairwise LD plot. |
network |
Generate Haplotype Net Relationshop with Haplotype Result |
pheno |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
plink.pedmap2hap |
plink.pedmap2hap |
plotEFF |
plotEFF |
plotHapNet |
plotHapNet |
plotHapTable |
plotHapTable |
plotHapTable2 |
plotHapTable2 |
plot_LDheatmap |
This function produces a pairwise LD plot. |
seqs |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
seqs2hap |
Generate Hap Results from Seqs |
SetATGas0 |
Set Position of ATG as Zero |
siteEFF |
Calculation of Sites Effective |
sites |
Add Infomation to Haplotype Results |
sites_compar |
sites comparison |
table2hap |
table2hap |
trimSeqs |
Generate Hap Results from Seqs |
vcf |
Datasets 'gff' contains a example of gff file used for test of visualization mutations on gene model. |
vcf2hap |
Generat Haps from VCF |
write.hap |
Save Haplotype Results to Disk |