get_lod_peaks: Get the LOD peaks for a dataset.

In churchill-lab/qtl2api: QTL2 API Library

Get the LOD peaks for a dataset.

Description

By default, this will get all LOD peaks stored in the 'dataset$lod_peaks' 'list'. If 'intcovar' is specified, only the peaks for that are returned.

Usage

get_lod_peaks(ds)

Arguments

ds	The dataset object to get the LOD peaks for.

Value

A named 'list' of all the LOD peaks. Each element in the 'list' is a 'tibble' with the following columns depending upon 'dataset$datatype':

• mRNA - 'marker,chr,pos,gene_id,symbol,gene_chrom,middle,lod'

• protein - 'marker,chr,pos,protein_id,gene_id,symbol,gene_chrom,middle,lod'

• phenotype - 'marker,chr,pos,data_name,short_name,description,lod'

If the allele effects are stored, values 'A-H' will also be included.

churchill-lab/qtl2api documentation built on April 17, 2025, 3:27 a.m.