Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

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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