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", "ri8selfIRIP1", "ri8sib", "bgmagic16"),
na.strings=c("-","NA"), rotate=FALSE, ...)
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.
Directory in which the data files will be found. In
Windows, use forward slashes ("/"
) or double backslashes
("\\"
) to specify directory trees.
Comma-delimited file for the RIL, in the "csv"
format described in the help file for read.cross
.
File with founder strains' genotypes, in the same
orientation as the rilfile
, but with just marker names and the
founders' marker genotypes.
The type of RIL.
A vector of strings which are to be interpreted as
missing values. For the
csv
formats, these are interpreted globally
for the entire
file, so missing value codes in phenotypes must not be valid
genotypes, and vice versa. For the gary
format, these are
used only for the phenotype data.
If TRUE, the rilfile
and founderfile
are
rotated (really transposed), with rows corresponding to markers
and columns corresponding to individuals.
Additional arguments, passed to the function
read.table
in the case of
csv
and csvr
formats. In particular, one may use the
argument
sep
to specify the field separator (the default is a comma)
and dec
to specify the character used for the decimal point
(the default is a period).
Karl W Broman, broman@wisc.edu
The rilfile
should include a phenotype cross
containing
character strings of the form ABCDEFGH
, indicating the cross
used to generate each RIL. The genotypes should be coded as
integers (e.g., 1 and 2).
The founder strains in the founderfile
should be the strains
A
, B
, C
, ..., as indicated in the cross
phenotype.
The default arrangement of the files is to have markers as columns and
individuals/founders as rows. If rotate=TRUE
, do the opposite:
markers as rows and individuals/founders as columns.
read.cross
, sim.cross
if (FALSE) {
ril <- read.cross("../Data", "ril_data.csv", "founder_geno.csv", "ri4self",
rotate=TRUE)}
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