segmentsListByDistance: 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 gaps in the genome.

Usage

segmentsListByDistance(
  bedmatrix,
  gap = 0.5,
  minMarkers = 50,
  nbSegments = 20,
  unit = "cM",
  verbose = TRUE
)

Arguments

bedmatrix	a bed.matrix object
gap	the minimum gap after which a segment is created
minMarkers	the minimum number of markers in a mini-segment
nbSegments	the number of mini-segments which the segment will be split
unit	the gap unit, "cM" (centirmorgans) or "Mb" (million of bases)
verbose	if TRUE, displays information on the process

Details

This function is used to create an object of class snpsSegments. It contains a list of segments delimited by gaps between available markers. Each segment is split in nbSegments mini-segments.

A segment is not split if it would result in mini-segments shorter that minMarkers. The indices in the mini-segments correspond to SNPs in bedmatrix.

Value

an snpsSegments object

See Also

Fantasio, segmentsListByDistance

Examples

 
#Please refer to vignette 

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