quick_peak: Fast peak finder in GWAS data
In myles-lewis/locuszoomr: Gene Locus Plot with Gene Annotations

quick_peak

R Documentation

Fast peak finder in GWAS data

Description

Simple but fast function for finding peaks in genome-wide association study (GWAS) data based on setting a minimum distance between peaks.

Usage

quick_peak(
  data,
  npeaks = NA,
  p_cutoff = 5e-08,
  span = 1e+06,
  min_points = 2,
  chrom = NULL,
  pos = NULL,
  p = NULL
)

Arguments

`data`	GWAS dataset (data.frame or data.table)
`npeaks`	Number of peaks to find. If set to `NA`, algorithm finds all distinct peaks separated from one another by region size specified by `span`.
`p_cutoff`	Specifies cut-off for p-value significance above which p-values are ignored.
`span`	Minimum genomic distance between peaks (default 1 Mb)
`min_points`	Minimum number of p-value significant points which must lie within the span of a peak. This removes peaks with single or only a few low p-value SNPs. To disable set `min_points` to 1 or less.
`chrom`	Determines which column in `data` contains chromosome information. If `NULL` tries to autodetect the column.
`pos`	Determines which column in `data` contains position information. If `NULL` tries to autodetect the column.
`p`	Determines which column in `data` contains SNP p-values. If `NULL` tries to autodetect the column.

Details

This function is designed for speed. SNP p-values are filtered to only those which are significant as specified by p_cutoff. Each peak is identified as the SNP with the lowest p-value and then SNPs in proximity to each peak within the distance specified by span are removed. Regions such as the HLA whose peaks may well be broader than span may produce multiple entries.