| write.cross {qtl} | R Documentation |
Data for a QTL experiment is written to a file (or files).
write.cross(cross, format=c("csv","mm","qtlcart","gary"),
filestem="data", chr, digits=5)
cross |
An object of class cross. See
read.cross for details. |
format |
Specifies whether to write the data in comma-delimited, Mapmaker, QTL Cartographer, or Gary Churchill's format. |
filestem |
A character string giving the first part of the output
file names (the bit before the dot). In Windows, use forward
slashes ("/") or double backslashes ("\\") to
specify directory trees. |
chr |
A vector specifying for which chromosomes genotype data should be written. |
digits |
Number of digits to which phenotype values should be rounded. |
Comma-delimited format: a single csv file is created in the format
read by read.cross.
Mapmaker format: Data is written to two files.
Suppose filestem="file". Then "file.raw" will contain
the genotype and phenotype data, and "file.prep" will contain
the necessary code for defining the chromosome assignments, marker
order, and inter-marker distances.
QTL Cartographer format: Data is written to two files. Suppose
filestem="file". Then "file.cro" will contain
the genotype and phenotype data, and "file.map" will contain
the genetic map information. Note that cross types are converted to
QTL Cartographer cross types as follows: riself to RF1, risib to RF2,
bc to B1 and f2 to RF2.
Gary's format: Data is written to six files. They are:
"geno.data" - genotype data;
"pheno.data" - phenotype data;
"chrid.dat" - the chromosome identifier for each marker;
"mnames.txt" - the marker names;
"markerpos.txt" - the marker positions;
"pnames.txt" - the phenotype names
Karl W Broman, kbroman@jhsph.edu; Hao Wu; Brian S. Yandell
## Not run: data(fake.bc) # comma-delimited format write.cross(fake.bc, "csv", "Data/fakebc", c(1,5,13)) # Mapmaker format write.cross(fake.bc, "mm", "Data/fakebc", c(1,5,13)) # QTL Cartographer format write.cross(fake.bc, "qtlcart", "Data/fakebc", c(1,5,13)) # Gary's format write.cross(fake.bc, "gary", c(1,5,13))## End(Not run)