read_ibd {skater} | R Documentation |
Read IBD segment file
Description
Reads in the inferred IBD segments from hapibd
(documentation) or IBD segment file generated by ped-sim
(documentation).
If reading a hapibd
segment file, the input data should have the following columns:
First sample identifier
First sample haplotype index (1 or 2)
Second sample identifier
Second sample haplotype index (1 or 2)
Chromosome
Base coordinate of first marker in segment
Base coordinate of last marker in segment
cM length of IBD segment
If read a pedsim
segment file, the input data should have the following columns:
First sample identifier
Second sample identifer
Chromosome
Physical position start
Physical position end
IBD type
Genetic position start
Genetic position end
Genetic length (end - start)
Usage
read_ibd(file, source)
Arguments
file |
Input file path |
source |
Source of the input file; must be one of |
Value
if source="hapibd"
, a tibble is returned.
If source="pedsim"
, a list with two tibble elements, IBD1
and IBD2
is returned.
Both the hapibd
tibble, and the two pedsim
tibbles contain six columns:
id1 (sample identifier 1)
id2 (sample identifier 2)
chr (chromosome)
start (segment bp start coordinate)
end (segment bp end coordinate)
length (shared segment length in genetic units, cM)
References
https://github.com/browning-lab/hap-ibd#output-files
https://github.com/williamslab/ped-sim#output-ibd-segments-file
Examples
hapibd_fp <- system.file("extdata", "GBR.sim.ibd.gz", package="skater", mustWork=TRUE)
hapibd_seg <- read_ibd(hapibd_fp, source = "hapibd")
pedsim_fp <- system.file("extdata", "GBR.sim.seg.gz", package="skater", mustWork=TRUE)
pedsim_seg <- read_ibd(pedsim_fp, source = "pedsim")