plot_LD: Plot a subset of the LD matrix

In RajLabMSSM/echoLD: echoverse module: LD downloading and processing

Plot a subset of the LD matrix

Description

Plot a heatmap of pairwise LD between SNPs.

Usage

plot_LD(
  LD_matrix,
  query_dat,
  span = 10,
  method = c("stats", "gaston", "graphics"),
  ...
)

Arguments

LD_matrix	LD matrix.
query_dat	SNP-level summary statistics subset to query the LD panel with.
span	This is very computationally intensive, so you need to limit the number of SNPs with span. If span=10, only 10 SNPs upstream and 10 SNPs downstream of the lead SNP will be plotted.
method	Method to use for plotting: "stats" : heatmap "gaston" : LD.plot "graphics" : image
...	Additional arguments passed to plotting function.

See Also

Other LD: check_population_1kg(), compute_LD(), filter_LD(), get_LD(), get_LD_1KG(), get_LD_1KG_download_vcf(), get_LD_UKB(), get_LD_matrix(), get_LD_vcf(), get_locus_vcf_folder(), ldlinkr_ldproxy_batch(), popDat_1KGphase1, popDat_1KGphase3, rds_to_npz(), saveSparse(), save_LD_matrix(), snpstats_get_MAF()

Examples

query_dat<- echodata::BST1
LD_matrix <- echodata::BST1_LD_matrix
echoLD::plot_LD(LD_matrix = LD_matrix,
                query_dat= query_dat)

RajLabMSSM/echoLD documentation built on May 12, 2024, 3:23 a.m.