gtable_ld_associations_gdata: Gtable of linkage disequilibrium and associations using a...

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Gtable of linkage disequilibrium and associations using a GenotypeData object

Description

Compute linkage disequilibrium using snprelate_ld on the set of SNPs in the associations data frame and call gtable_ld_associations. Creates a gtable of a linkage disequilibrium, chromosomic positions, and association scores ggplots.

Usage

gtable_ld_associations_gdata(
  df_assocs,
  gdata,
  pvalue_colname = "pvalues",
  labels_colname = "probe_id",
  diamonds = nrow(df_assocs) <= 40,
  window = 15,
  ...
)

Arguments

df_assocs	SNP annotation data frame with columns chromosome, position, and as specified by parameters pvalue_colname and optionally labels_colname.
gdata	GenotypeData object, as returned by load_gds_as_genotype_data
pvalue_colname	Column name of df_snp with association values
labels_colname	Optional column name of df_snp with labels. Set NULL to remove labels.
diamonds	Should the values be displayed as diamonds or points ? Default is TRUE for up to 40 SNPs.
window	Window size for snprelate_ld. Forced to the total number of SNPs if diamonds is FALSE
...	Passed to gtable_ld_associations

Value

gtable

snplinkage documentation built on May 4, 2023, 9:09 a.m.