chisq_pvalues_gdata {snplinkage}

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