This function performing filters on X variants based on Y subjects for TWAS analysis. This function checks whether the absence (NA) of certain subjects would lead to monomorphic in some variants in X after removing of these subjects data from X.

This function performing filters on X variants based on Y subjects for TWAS analysis. This function checks whether the absence (NA) of certain subjects would lead to monomorphic in some variants in X after removing of these subjects data from X.

Usage

filter_X_with_Y(
  X,
  Y,
  missing_rate_thresh,
  maf_thresh,
  var_thresh = 0,
  maf = NULL,
  X_variance = NULL
)

Arguments

missing_rate_thresh

Maximum individual missingness cutoff.

maf_thresh

Minimum minor allele frequency (MAF) cutoff.

var_thresh

Minimum variance cutoff for a variant. Default is 0.

X_variance

A vector of variance for X variants.