ceGWAS: The central object of cegwas2

In AndersenLab/cegwas2: C. elegans genome-wide association

Description

The central object of cegwas2

Usage

ceGWAS

Format

R6Class object.

Fields

trait_name

name of trait, extracted from input data frame

strains

name of strains provided in input data frame

phenotype

phenotypes provided by the user

processed_phenotype

output generated by process_phenotypes

mapping

output generated by perform_mapping

peak_intervals

identified confidence intervals

fine_mapping

more details to come as we create methods

snvs

snv set

K

kinship matrix

Methods

Documentation

For full documentation of each method go to https://github.com/AndersenLab/cegwas2

new(phenotype)

This method is used to create object of this class with phenotype, which is a two-column data frame with colnames strain and trait. Trait name can be user specified

set_markers(genotype_matrix)

This method sets genotype matrix to something other than the default provided by cegwas2. This will also generate a corresponding kinship matrix

run_mapping(...)

This method executes the perform_mappng function from cegwas2

AndersenLab/cegwas2 documentation built on Aug. 26, 2020, 4:43 p.m.