First step {eqtl}R Documentation

Importing the data

Description

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.

The physical data of the genetic map

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:

The coordinates of the expression traits

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.

Author(s)

Hamid A khalili


[Package eqtl version 1.0 Index]