gtable_ld_gdata: Gtable of linkage disequilibrium and positions using a...

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Gtable of linkage disequilibrium and positions using a GenotypeData object

Description

Compute linkage disequilibrium using snprelate_ld on a set of SNP indexes and call gtable_ld. Two parameters are available to compute and compare minor allele frequency filtering and TagSNP selection by displaying two LD plots with their positions in the center. The maf and r2 parameters are used similarly and as follows: - compare baseline with MAF 5 gtable_ld(gdata, snps_idx, maf = 0.05) - compare baseline with TagSNP r2 = 0.8 gtable_ld(gdata, snps_idx, r2 = 0.8) - compare 5 gtable_ld(gdata, snps_idx, maf = c(0.05, 0.05), r2 = 0.8) - compare MAF 5 gtable_ld(gdata, snps_idx, maf = c(0.05, 0.1), r2 = c(0.8, 0.6))

Usage

gtable_ld_gdata(
  gdata,
  snps_idx,
  maf = NULL,
  r2 = NULL,
  diamonds = length(snps_idx) < 40,
  window = 15,
  autotitle = TRUE,
  autotitle_bp = TRUE,
  double_title = FALSE,
  ...
)

Arguments

gdata	GenotypeData object returned by load_gds_as_genotype_data
snps_idx	SNPs indexes to select
maf	Minor allele frequency threshold(s), see description
r2	TagSNP r2 threshold(s), see description
diamonds	Display the values as diamonds or as points Default is TRUE for less than 40 SNPs.
window	Window size for snprelate_ld. Forced to the total number of SNPs if diamonds is FALSE
autotitle	Set title to feature selection method(s), number of SNPs and chromosome
autotitle_bp	Set biplot title to feature selection method(s), number of SNPs and chromosome
double_title	Logical, if false (default) keep only biplot title
...	Passed to gtable_ld

Value

gtable of ggplots

Examples

library(snplinkage)
gds_path <- save_hgdp_as_gds()
gdata <- load_gds_as_genotype_data(gds_path)
qc <- snprelate_qc(gdata, tagsnp = .99)

snp_idxs_1p13_large <- select_region_idxs(qc$gdata, chromosome = 1,
  position_min = 114e6, n_snps = 100)
plt <- gtable_ld_gdata(qc$gdata, snp_idxs_1p13_large)

snplinkage documentation built on Sept. 11, 2024, 6:02 p.m.