readMWril {qtl} | R Documentation |
Data for a set of 4- or 8-way recombinant inbred lines (RIL) is read
from a pair of comma-delimited files and converted
into an object of class cross
.
We require chromosome
assignments for the genetic markers, and assume that markers are in
their correct order.
readMWril(dir="", rilfile, founderfile, type=c("ri4self", "ri4sib", "ri8self", "ri8sib", "bgmagic16"), na.strings=c("-","NA"), rotate=FALSE, ...)
dir |
Directory in which the data files will be found. In
Windows, use forward slashes ( |
rilfile |
Comma-delimited file for the RIL, in the |
founderfile |
File with founder strains' genotypes, in the same
orientation as the |
type |
The type of RIL. |
na.strings |
A vector of strings which are to be interpreted as
missing values. For the
|
rotate |
If TRUE, the |
... |
Additional arguments, passed to the function
|
The rilfile
should include a phenotype cross
containing
character strings of the form ABCDEFGH
, indicating the cross
used to generate each RIL.
The founder strains in the founderfile
should be the strains
A
, B
, C
, ..., as indicated in the cross
phenotype.
An object of class cross
; see the help file for
read.cross
for details.
An additional component crosses
is included; this is a matrix
indicating the crosses used to generate the RIL.
Karl W Broman, kbroman@biostat.wisc.edu
## Not run: ril <- read.cross("../Data", "ril_data.csv", "founder_geno.csv", "ri4self", rotate=TRUE) ## End(Not run)