Man pages for snplinkage
Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

chisq_pvaluesCompute Chi-squared p-values
chisq_pvalues_gdataCompute Chi-squared p-values on a Genotype data object
compoundAssignment pipe
crohnCrohn's disease data
diamond_annotsGet diamond ggplot layer.
expositionExposition pipe
fetch_allele1.defaultFetch allele 1 (default object)
fetch_allele1.GdsGenotypeReaderFetch allele 1 (GdsGenotypeReader object)
fetch_allele1.GenotypeDataFetch allele 1 (GenotypeData object)
fetch_allele1.GenotypeDataSubsetFetch allele 1 (GenotypeDataSubset object)
fetch_allele2.defaultFetch allele 2 (default object)
fetch_allele2.GdsGenotypeReaderFetch allele 2 (GdsGenotypeReader object)
fetch_allele2.GenotypeDataFetch allele 2 (GenotypeData object)
fetch_allele2.GenotypeDataSubsetFetch allele 1 (GenotypeDataSubset object)
fetch_gds.defaultFetch GDS (default)
fetch_gds.GdsGenotypeReaderFetch GDS (GdsGenotypeReader)
fetch_gds.GenotypeDataFetch GDS (GenotypeData)
fetch_gds.GenotypeDataSubsetFetch GDS (GenotypeDataSubset)
gdata_add_gene_annotsgdata_add_gene_annots
gdata_add_gene_annots_aim_examplegdata_add_gene_annots_aim_example
gdata_add_gene_annots_hladr_examplegdata_add_gene_annots_hladr_example
gdata_scans_annotsgdata_scan_annots
gdata_snps_annotsgdata_snp_annots
get_biomart_metadbget_biomart_metadb
get_scan_annot.GenotypeDataGet scans annotations (GenotypeData object)
get_scan_annot.GenotypeDataSubsetGet scans annotations (GenotypeDataSubset object)
get_snp_annot.GenotypeDataGet SNPs annotations (GenotypeData object)
get_snp_annot.GenotypeDataSubsetGet SNPs annotations (GenotypeDataSubset object)
ggplot_associationsGgplot associations
ggplot_ldGgplot linkage disequilibrium
ggplot_snp_posGgplot SNPs position
gtable_ldGtable of linkage disequilibrium and chromosomic positions
gtable_ld_associationsGtable of linkage disequilibrium and associations
gtable_ld_associations_combineBuild gtable by combining ggplots
gtable_ld_associations_gdataGtable of linkage disequilibrium and associations using a...
gtable_ld_gdataGtable of linkage disequilibrium and positions using a...
gtable_ld_grobsBuild gtable by combining ggplots
is_snp_first_dim.defaultIs SNP first dimension (default)
is_snp_first_dim.gds.classIs SNP first dimension (GDS object)
is_snp_first_dim.GdsGenotypeReaderIs SNP first dimension (GdsGenotypeReader object)
is_snp_first_dim.GenotypeDataIs SNP first dimension (GenotypeData object)
is_snp_first_dim.MatrixGenotypeReaderIs SNP first dimension (MatrixGenotypeReader object)
is_snp_first_dim.NcdfGenotypeReaderIs SNP first dimension (NcdfGenotypeReader object)
load_gds_as_genotype_dataLoad GDS as Genotype Data
parallel_applySeparate a matrix in a list of matrices of length the number...
pipePipe
print_qc_as_tex_tableprint_qc_as_tex_table
save_hgdp_as_gdssave_hgdp_as_gds
select_region_idxsselect_region_idxs
snplinkage-packagesnplinkage: Single Nucleotide Polymorphisms Linkage...
snprelate_allele_frequenciesCompute allele frequencie and snp missing rate
snprelate_ldWrapper for snpgdsLDMat to compute r2
snprelate_ld_selectWrapper for snpgdsLDpruning to select Tag SNPs
snprelate_qcsnprelate_qc
snplinkage documentation built on Sept. 11, 2024, 6:02 p.m.