write.cross: Write data for a QTL experiment to a file

In kbroman/qtl: Tools for Analyzing QTL Experiments

Write data for a QTL experiment to a file

Description

Data for a QTL experiment is written to a file (or files).

Usage

write.cross(cross, format=c("csv", "csvr", "csvs", "csvsr",
                            "mm", "qtlcart", "gary", "qtab",
                            "mapqtl", "tidy"),
            filestem="data", chr, digits=NULL, descr)

Arguments

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, Gary Churchill's, QTAB, MapQTL 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 and genetic map positions should be rounded. If NULL (the default), they are not rounded.
descr	Character string description; used only with format="qtab".

Details

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

QTAB format: See documentation.

MapQTL format: See documentation.

Tidy format: Data is written to three files, "stem_gen.csv", "stem_phe.csv", and "stem_map.csv" (where stem is taken from the filestem argument.

Author(s)

Karl W Broman, [e-mail]; Hao Wu; Brian S. Yandell; Danny Arends; Aaron Wolen

See Also

read.cross

Examples

## 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) 

kbroman/qtl documentation built on Jan. 13, 2024, 10:14 p.m.