First step {eqtl} | R Documentation |
R/eqtl needs to import some data in addition to those necessary for R/qtl package: the physical data of the genetic markers and the phycical coordinates of the probes used to measure the expression traits.
This is a simple data frame with columns "Marker"
,"chr"
and "PP"
as described for BSpgmap
dataset. You can import these data by the way you wanted to obtain this data frame. I describes here one simple way to import it from a file:
cross
object (here seed10
). The markers must appear in the same order as the markers and chromosomes in the cross
object (in the order of the map !)."Marker","chr","PP"
"MSAT100008",1,8639
"T1G11",1,1243250
"F21M12",1,3212191
"IND4992",1,4992444
"IND6375",1,6375557
"MSAT1.10",1,7296649
"MSAT108193",1,8192951
cross
object: seed10.cleaned$geno$'1'$map
seed10.cleaned$geno$'2'$map
seed10.cleaned$geno$'3'$map
a_new_BSpgmap <- read.table("path to the file",header=TRUE,sep=",")
This is a simple data frame with columns "etrait.name"
,"chr"
, "start"
and "stop"
as described for CATMA.coord
. By the same way than the map data importation, you can do by the way you wanted. The importation process is quite similar. Here the file can describe more expression trait than the phenotypes described in cross
object. Of course all etraits described in cross
object must have coordinates in the file.
"etrait.name","chr","start","stop"
"CATMA1A00010",1,4707,4972
"CATMA1A00020",1,6442,6653
"CATMA1C71002",1,7579,7791
"CATMA1A00030",1,12268,12486
"CATMA1A00035",1,30923,31142
"CATMA1A00040",1,31232,31381
"CATMA1A00045",1,33814,34211
"CATMA1A00050",1,38785,38971
cross
object:names(seed10.cleaned$phe)[1:10]
new_CATMA.coord <- read.table('./data_Files/listGST-coord.tab', sep="\t", header= TRUE)
Hamid A khalili