magnusdv
commented
2 years ago There are (at least) two natural ways to interprete dist:
1) Imagine the chromosomes being glued together as a long string, and place markers every dist units apart.
2) On each chromosome, place a marker at one end, and then every dist units apart.
Method 1) always gives floor(L/dist) + 1 markers, where L is the sum of chromosome lengths. On the other hand, it uses a nonsensical notion of distance between loci on different chromosomes.
Method 2) always gives at least one marker per chromosome. This is the approach currently implemented.
I guess I could include 1) also if it turns out to be important.
Return an error or only one marker if
distexceeds the the total chromosome length?:library(pedtools) x = distributeMarkers(nuclearPed(), dist = 3000, prefix = "M") getMap(x)
> CHROM MARKER MB
> 1 1 M1 0
> 2 2 M2 0
> 3 3 M3 0
> 4 4 M4 0
> 5 5 M5 0
> 6 6 M6 0
> 7 7 M7 0
> 8 8 M8 0
> 9 9 M9 0
> 10 10 M10 0
> 11 11 M11 0
> 12 12 M12 0
> 13 13 M13 0
> 14 14 M14 0
> 15 15 M15 0
> 16 16 M16 0
> 17 17 M17 0
> 18 18 M18 0
> 19 19 M19 0
> 20 20 M20 0
> 21 21 M21 0
> 22 22 M22 0
Created on 2022-03-29 by the reprex package (v2.0.1)