dlmap.convert.cross {dlmap}R Documentation

Convert input files to dlmap input format

Description

Reads in files from all formats supported by read.cross and converts them to dlmap input format. Creates dlmap input files in working directory.

Usage

dlmap.convert.cross(format = c("csv", "csvr", "csvs", "csvsr", "mm", "qtx", 
"qtlcart", "gary", "karl", "rqtl"), obj, pheobj, idname="ID", dir = "", 
genoutfile = "dlgenin.dat", pheoutfile = "dlphein.dat", 
mapoutfile = "dlmapin.dat", file, genfile, mapfile, phefile, 
chridfile, mnamesfile, pnamesfile, na.strings = c("-", "NA"),
genotypes = c("A", "H", "B", "D", "C"), alleles = c("A", "B"), ...)

Arguments

format See documentation for read.cross. Also supports the input of an object of class cross ("rqtl" format)
obj if format="rqtl", object of class cross
pheobj Data frame or matrix containing supplementary spatial/environmental data
idname Unique identifier variable name; will be used to match phenotypic and marker data
dir Directory where input files are located; default is working directory
genoutfile File with genotype data output in dlmap input format
pheoutfile File with phenotype data output in dlmap input format
mapoutfile File with marker position information output in dlmap input format
file see read.cross
genfile see read.cross
mapfile see read.cross
phefile see read.cross
chridfile see read.cross
mnamesfile see read.cross
pnamesfile see read.cross
na.strings see read.cross
genotypes see read.cross
alleles see read.cross
... additional arguments to read.cross

Details

Use of this function will allow automatic input into dlmap.asreml or dlmap.lme. Otherwise input files will need to be constructed by hand. See below for the format if constructing input manually.

If a single set of trait values is available for each genotype, then phenotypic data will be input through the arguments obj, file, or phefile (depending on the file format). The argument envobj allows for input of phenotypic data on replicates or additional individuals which are not necessarily genotyped.

Value

Nothing returned. Three files output into names specified by genoutfile, pheoutfile and mapoutfile (or default values of "dlgenin.dat", "dlphein.dat", "dlmapin.dat" if these arguments are missing).

Notation:
n.gen is the number of genotyped individuals
n.ind is the number of phenotyped individuals
n.obs is the number of phenotypic observations (for a single trait)
M is the number of markers
P is the number of phenotypes
C is the number of chromosomes

Note that in general n.gen <= n.ind <= n.obs since there may be multiple observations per individual, and more individuals may be phenotyped than genotyped. Individuals which are genotyped but not phenotyped will not be considered in analysis.


Genotypes
The genotype data file genoutfile has a header row with the name of the unique identifier variable and the marker names. This is followed by n.gen rows containing the identifier and genotypes for each individual.

ID mrk1 ... mrkM
1 1 ... 1
... ...
n.gen 0 ... 1

Phenotypes
The phenotype data file pheoutfile has a header row with the name of the unique identifier variable and the phenotype names. This is followed by n.obs rows containing the identifier and phenotypes for each sample. If envobj is not input, the number of rows in this file will correspond to the number of rows in genoutfile.

ID phename1 ... phenameP
1 3.7 ... 2.4
... ...
n.ind 5.1 ... 8.2

Linkage Map
The map data file mapoutfile has a header row with the labels shown below for the marker ID, chromosome and position in cM. The third column can be omitted, in which case the marker positions will be estimated from the data. Note: the marker names must be in the same order as in the genotype data file.

MrkID Chr Pos
mrk1 1 0.00
...
mrkM C 100.0

Author(s)

Emma Huang and Andrew George

References

Huang, BE and George, AW. Look before you leap: A new approach to QTL mapping. Manuscript in preparation

See Also

read.cross

Examples

# load dataset
data(BSdat)
data(BSphen)

## Not run: 
# convert data to dlmap format
dlmap.convert.cross(format="rqtl", obj=BSdat)

# convert data with separate phenotypic trait file
dlmap.convert.cross(format="rqtl", obj=BSdat, envobj=BSphen, idname="ID")
## End(Not run)

[Package dlmap version 1.0 Index]