segmentsListByHotspots: Creation of a list of segments

In genostats/Fantasio: Genetic Data Analyses in Presence of Inbreeding

Creation of a list of segments

Description

Creates a list of segments delimited by recombination hotspots

Usage

segmentsListByHotspots(
  bedmatrix,
  intensity = 10,
  hotspots = hotspot_hg19,
  minMarkers = 0,
  verbose = TRUE
)

Arguments

bedmatrix	a bed.matrix object
intensity	hotspots intensity threshold in cM/Mb
hotspots	a data frame of recombination rates
minMarkers	minimum number of markers in a segment
verbose	if TRUE, displays information on the process

Details

This function creates an object of class hotspots.segments, containing a list of segments delimited by hotspots. The object is a list of list of vectors indices of SNPs. There are as many sublists as chromosomes. The indices correspond to SNPs in bedmatrix.

The user can provide a hotspots data frame with a format similar to hotspot_hg19.

Value

an hotspots.segments object

See Also

Fantasio, segmentsListByDistance

Examples

 
#Please refer to vignette

genostats/Fantasio documentation built on Feb. 2, 2023, 5:28 p.m.