gtable_ld_associations_gdata {snplinkage}

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