HBDPlotId | R Documentation |
This function plots HBDsegments or ROHs for all the chromosoms of a given individual
HBDPlotId(Submaps, ROH, unit = "cM", id, famid, regions, outfile, build = 37)
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) |
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
A plot of the individual's HBDsegments.
#Please refer to vignette
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