chisq_pvalues_gdata: Compute Chi-squared p-values on a Genotype data object

In snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Compute Chi-squared p-values on a Genotype data object

Description

Compute Chi-squared p-values on a Genotype data object

Usage

chisq_pvalues_gdata(
  gdata,
  snp_idxs,
  response_column = "region",
  response_value = "Europe",
  threshold = 2,
  ...
)

Arguments

gdata	Genotype data object
snp_idxs	SNPs indexes
response_column	Response column in gdata scans annotations data frame
response_value	Response value. The response vector will be a logical, true if equal to the value, false otherwise.
threshold	Keep only associations greater than the threshold
...	Passed to chisq_pvalues

Value

SNPs annotation data frame, chi-squared p-values in column pvalues

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