testInteraction: Test for interaction between genotype and condition using...

In kauralasoo/seqUtils:

Description

Test for interaction between genotype and condition using ANOVA model

Usage

testInteraction(gene_id, snp_id, trait_matrix, sample_metadata, vcf_file,
  qtl_formula, interaction_formula, return_value = "ponly")

Arguments

gene_id	Tested gene id
snp_id	Tested SNP id
trait_matrix	expression or chromatin accessibility matrix
sample_metadata	data frame with sample metadata and covariates
vcf_file	VCF file from gdsToMatrix() function
qtl_formula	Formula for the model with just genotype and condition terms
interaction_formula	Formula for the model with interaction term betweeb genotype and condition

Value

Either a pvalue (if return_value == "ponly") or the full linear model object.

kauralasoo/seqUtils documentation built on May 20, 2019, 7:42 a.m.