snplinkage (version 1.2.0)

gtable_ld_gdata: 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,
  ...
)

Value

gtable of ggplots

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

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)