# Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

## Documentation for package ‘snplinkage’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

%$% | Exposition pipe
%<>% | Assignment pipe
%>% | Pipe
chisq_pvalues | Compute Chi-squared p-values
chisq_pvalues_gdata | Compute Chi-squared p-values on a Genotype data object
diamond_annots | Get diamond ggplot layer.
gdata_add_gene_annots | gdata_add_gene_annots
gdata_add_gene_annots_aim_example | gdata_add_gene_annots_aim_example
gdata_add_gene_annots_hladr_example | gdata_add_gene_annots_hladr_example
gdata_scans_annots | gdata_scan_annots
gdata_snps_annots | gdata_snp_annots
get_biomart_metadb | get_biomart_metadb
ggplot_associations | Ggplot associations
ggplot_ld | Ggplot linkage disequilibrium
ggplot_snp_pos | Ggplot SNPs position
gtable_ld | Gtable of linkage disequilibrium and chromosomic positions
gtable_ld_associations | Gtable of linkage disequilibrium and associations
gtable_ld_associations_gdata | Gtable of linkage disequilibrium and associations using a GenotypeData object
gtable_ld_gdata | Gtable of linkage disequilibrium and positions using a GenotypeData object
load_gds_as_genotype_data | Load GDS as Genotype Data
parallel_apply | Separate a matrix in a list of matrices of length the number of cores and apply a function on the columns in parallel
print_qc_as_tex_table | print_qc_as_tex_table
save_hgdp_as_gds | save_hgdp_as_gds
select_region_idxs | select_region_idxs
snprelate_allele_frequencies | Compute allele frequencie and snp missing rate
snprelate_ld | Wrapper for snpgdsLDMat to compute r2
snprelate_ld_select | Wrapper for snpgdsLDpruning to select Tag SNPs
snprelate_qc | snprelate_qc