| read.cross.mm {qtl} | R Documentation |
Data for a QTL experiment is read from a set of files and converted
into an object of class cross.
read.cross.mm(dir,rawfile,mapfile,estimate.map)
dir |
Character string specifying the directory containing the input files. |
rawfile |
Mapmaker rawfile containing the genotype and phenotype
data. Rows beginning with the symbol # are ignored. The
first line should be either data type f2 intercross or
data type f2 backcross. The second line should begin with
three numbers indicating the numbers of individuals, markers and
phenotypes in the file. This line may include the word
symbols followed by symbol assignments (see the documentation
for mapmaker, and cross your fingers). The rest of the lines give
genotype data followed by phenotype data, with marker and phenotype
names always beginning with the symbol *.
|
mapfile |
File containing two or three columns separated by white space, with no header row. The first column gives the chromosome assignments. The second column gives the marker names, with markers listed in the order along the chromosomes. An optional third column lists the map positions of the markers. |
estimate.map |
If mapfile does not contain the markers' map
positions and estimate.map is TRUE, the genetic map
for the cross is estimated using the function est.map. |
We use the marker names to infer the chromosome names (assuming that most marker names are like D1M120 or D19M99); if the markers look like DXM*, we assume it is the X chromosome. If all genotypes are <= 2, we assume it is a backcross, otherwise it is assumed to be an intercross. We weren't thinking about 4-way crosses, and so this format doesn't work for that type of cross.
An object of class cross. See read.cross for details.
Karl W Broman,
kbroman@jhsph.edu
http://biosun01.biostat.jhsph.edu/~kbroman/software/qtl.html
read.cross,
read.cross.karl,
read.cross.gary,
read.cross.csv
cross1 <- read.cross(format="mm", dir="Data", rawfile="sample.raw", mapfile="sample.map")