| write.cross {qtl} | R Documentation |
Data for a QTL experiment is written to a file (or files).
write.cross(cross, format=c("csv", "csvr", "csvs", "csvsr",
"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, rotated 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. This should be a vector of character strings
referring to chromosomes by name; numeric values are converted to
strings. Refer to chromosomes with a preceding - to have all
chromosomes but those considered. A logical (TRUE/FALSE) vector may
also be used. |
digits |
Number of digits to which phenotype values should be rounded. |
Comma-delimited formats: a single csv file is created in the formats
"csv" or "csvr". Two files are created (one for the
genotype data and one for the phenotype data) for the formats
"csvs" and "csvsr"; if filestem="file", the two
files will be names "file_gen.csv" and "file_phe.csv".
See the help file for read.cross for details on these formats.
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@biostat.wisc.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)) # rotated comma-delimited format write.cross(fake.bc, "csvr", "Data/fakebc", c(1,5,13)) # split comma-delimited format write.cross(fake.bc, "csvs", "Data/fakebc", c(1,5,13)) # split and rotated comma-delimited format write.cross(fake.bc, "csvsr", "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)