grab.locus.from.scan: Pulls loci from scan objects based on specified criteria

In gkeele/miqtl: Suite of QTL Mapping Functions

Pulls loci from scan objects based on specified criteria

Description

This function parses a scan object and returns loci, for instance, the locus with the minimum p-value.

Usage

grab.locus.from.scan(
  scan.object,
  use.lod = FALSE,
  chr = "all",
  criterion = c("min", "max"),
  return.value = c("marker", "position", "chr", "index")
)

Arguments

scan.object	A scan.h2lmm() object (ROP or multiple imputations). If multiple imputations, median and confidence interval on median are plotted.
use.lod	DEFAULT: FALSE. Specifies whether loci should be selected based on LOD scores or p-values.
chr	DEFAULT: "all". The portion of the scan that loci are being pulled from.
criterion	DEFAULT: "min". The criterion by which loci are selected. "min" selects the locus with the minimum statistical score. "max" selects the locus with the maximum statistical score.
return.value	DEFAULT: "marker". If "marker", returns the marker name. If "positions", returns the position in both cM and Mb. If "chr", returns the chr of the peak. If "index", returns the index of the vector.

Examples

grab.locus.from.scan()

gkeele/miqtl documentation built on Sept. 13, 2024, 5:49 a.m.