# Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

## Documentation for package ‘snplinkage’ version 1.2.0

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

## 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
crohn | Crohn's disease data
diamond_annots | Get diamond ggplot layer.
fetch_allele1.default | Fetch allele 1 (default object)
fetch_allele1.GdsGenotypeReader | Fetch allele 1 (GdsGenotypeReader object)
fetch_allele1.GenotypeData | Fetch allele 1 (GenotypeData object)
fetch_allele1.GenotypeDataSubset | Fetch allele 1 (GenotypeDataSubset object)
fetch_allele2.default | Fetch allele 2 (default object)
fetch_allele2.GdsGenotypeReader | Fetch allele 2 (GdsGenotypeReader object)
fetch_allele2.GenotypeData | Fetch allele 2 (GenotypeData object)
fetch_allele2.GenotypeDataSubset | Fetch allele 1 (GenotypeDataSubset object)
fetch_gds.default | Fetch GDS (default)
fetch_gds.GdsGenotypeReader | Fetch GDS (GdsGenotypeReader)
fetch_gds.GenotypeData | Fetch GDS (GenotypeData)
fetch_gds.GenotypeDataSubset | Fetch GDS (GenotypeDataSubset)
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
get_scan_annot.GenotypeData | Get scans annotations (GenotypeData object)
get_scan_annot.GenotypeDataSubset | Get scans annotations (GenotypeDataSubset object)
get_snp_annot.GenotypeData | Get SNPs annotations (GenotypeData object)
get_snp_annot.GenotypeDataSubset | Get SNPs annotations (GenotypeDataSubset object)
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_combine | Build gtable by combining ggplots
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
gtable_ld_grobs | Build gtable by combining ggplots
is_snp_first_dim.default | Is SNP first dimension (default)
is_snp_first_dim.gds.class | Is SNP first dimension (GDS object)
is_snp_first_dim.GdsGenotypeReader | Is SNP first dimension (GdsGenotypeReader object)
is_snp_first_dim.GenotypeData | Is SNP first dimension (GenotypeData object)
is_snp_first_dim.MatrixGenotypeReader | Is SNP first dimension (MatrixGenotypeReader object)
is_snp_first_dim.NcdfGenotypeReader | Is SNP first dimension (NcdfGenotypeReader 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