ziplinR is a R package to project genome and genetic map positions from one map to another based on common features. It is especially useful to convert genetic positions (e.g. QTLs) from a genetic map to genomic physical positions, or to convert SNP physical coordinates into a pseudo genetic map.
Install devtools package if not already done
install.packages(devtools)
Load devtools then install ziplinR package
library(devtools)
install_github("jframi/ziplinR")
Then load ziplinR
library(ziplinR)
The package comes with 3 datasets:
- p118genet : is a reference genetic map developed on a large (400 individuals) F3 population with 227 Kasp markers and used for QTL detection in the following papers : 10.1016/j.jcs.2018.11.012 and 10.1016/j.fcr.2018.02.007
- genomv2 and genomv3 : are physical positions of ~1800 Kasp markers on sorghum genome v2 and v3 assemblies.
The main function is the ziplinR function that projects positions from one map to the other.
The positions to be projected need to be formatted as a map object from the qtl package using the as.map function.
Let's build a data.frame with a couple of positions from 2 chromosomes. In real life, this data.frame would be obtained from a file using read.table or data.table::fread. The names of columns doesn't matter but the order does as explained in ?as.map
positions <- data.frame(feat=c("mk1",
"qtl1-conf-int-1",
"qtl1-peak",
"qtl1-conf-int-2",
"mk2",
"qtl-feature-2"),
chrom=c(1,1,1,1,2,2),
pos=c(10, 12, 18, 24, 6, 140))
| feat | chrom | pos |
|---|---|---|
| mk1 | 1 | 10 |
| qtl1-conf-int-1 | 1 | 12 |
| qtl1-peak | 1 | 18 |
| qtl1-conf-int-2 | 1 | 24 |
| mk2 | 2 | 6 |
| qtl-feature-2 | 2 | 140 |
m <- as.map(positions)
m
#$`1`
# mk1 qtl1-conf-int-1 qtl1-peak qtl1-conf-int-2
# 10 12 18 24
#$`2`
# mk2 qtl-feature-2
# 6 140
This map can then be projected using two reference maps :
- map1 : a map that has the the same reference frame as the the positions you are going to project (in the case you are projecting QTL positions, it will be the genetic map that has been used for QTL detection)
- map2 : a map with a new reference frame (e.g physical map) and several (as many as possible) common markers with map1
NB that chromosome names of map, map1 and map2 have to be same, ie "1","2",..., "10" in this example.
mp <- ziplinR(map = m, map1 = p118.genet, map2=genomv3)
mp
#$`1`
# mk1 qtl1-conf-int-1 qtl1-peak qtl1-conf-int-2
# 3831182 4495059 8107227 11083608
#$`2`
# mk2 qtl-feature-2
# 1804105 70071134
The new map with projected positions can be converted back to a data.frame with something like:
data.frame(feat=unlist(lapply(mp, names)),
chr=unlist(lapply(seq_along(mp), function(a) rep(names(mp)[a],length(mp[[a]])))),
pos=unlist(mp))
| feat | chr | pos |
|---|---|---|
| mk1 | 1 | 3831182 |
| qtl1-conf-int-1 | 1 | 4495059 |
| qtl1-peak | 1 | 8107227 |
| qtl1-conf-int-2 | 1 | 11083608 |
| mk2 | 2 | 1804105 |
| qtl-feature-2 | 2 | 70071134 |