HBDPlotId: plot of HBD segment

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

plot of HBD segment

Description

This function plots HBDsegments or ROHs for all the chromosoms of a given individual

Usage

HBDPlotId(Submaps, ROH, unit = "cM", id, famid, regions, outfile, build = 37)

Arguments

Submaps	a list.submap object
ROH	(optional) a data frame from which the segments will be plotted
unit	the unit used to plot, "Bases" or "cM" (default is "CM")
id	the individual id of the individual wanted
famid	the family id of the individual wanted
regions	a specific region to be highlighted in the plot (optional)
outfile	a name for the plot (optional)
build	the value of the genome build to use to plot chromosome in the plot (35, 36, 37,or 38, default is 37)

Details

If 'ROH' is provided, it must be a data frame containing columns 'FID', 'IID', 'CHR', 'POS1', 'POS2', 'PHE'. Such a data frame can be obtained by reading the report generated by 'plink' with the option '–homozyg'. If 'ROH' is not provided, the function will plot HBD segments defined in the Submaps object.

The 'regions' argument is optional. If provided, it must be a matrix containing one line per region to be highlighted with in each line :

• the chromosome number

• start

• end

Value

A plot of the individual's HBDsegments.

Examples

 
#Please refer to vignette 

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