find_peaks: Find Peaks from GWAS Peaks

Description Usage Arguments Details Value

View source: R/process_mappings.R

Description

find_peaks Identifies QTL from GWAS mapping data set.

Usage

1
find_peaks(processed_mapping_df, CI_size = 50, snp_grouping = 200)

Arguments

processed_mapping_df

The first element of the output list from the calculate_VE function.

CI_size

defines the size (in # SNPs) of confidence intervals. Default is 50 and is defined in more detail below.

snp_grouping

defines grouping of peaks. Defined further below, default is 200.

Details

This function identifies QTL by looking at SNPs above the bonferroni corrected p-value. If only one SNP passed the significance cutoff, then the confidence interval is defined as +/- CI_size (number of SNPs; default 50) away from that SNP. If multiple SNPs are above the cutoff, the function asks if SNPs are within an arbitrary number of SNPs away snp_grouping - default 200. If the significant SNPs are within this range, they are grouped into the same peak. If they are greater than this distance, then the peaks are considered unique.

Value

Outputs a two element list that contains. First element - data frame containing all identified intervals Second element - list containing one element for each interval


AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.