dlcross {dlmap} | R Documentation |
Reads in files from all formats supported by read.cross
and converts them to dlmap input format. Also supports other formats for objects
dlcross(format = c("csv", "csvr", "csvs", "csvsr", "mm", "qtx", "qtlcart", "gary", "karl", "rqtl", "dlmap", "other"), genobj, pheobj, mapobj, idname="ID", dir = "", file, genfile, mapfile, phefile, chridfile, mnamesfile, pnamesfile, na.strings = c("-", "NA"), genotypes = c("A", "H", "B", "D", "C"), alleles = c("A", "B"), type, step=0, fixpos=0, estmap=TRUE, ...)
format |
See documentation for read.cross . Also supports the
input of an object of class cross ("rqtl" format), "dlmap" format
(described below) and continuous data for association mapping populations
("other" format) |
genobj |
if format="rqtl", object of class cross ;
if format="dlmap" or "other" data frame containing genotypes |
pheobj |
Data frame or matrix containing supplementary phenotypic or environmental data |
mapobj |
if format="other" or "dlmap", 2/3-columned data-frame containing marker names, chromosomes and marker positions |
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 |
file |
see read.cross |
genfile |
see read.cross ; if format="dlmap" see below |
mapfile |
see read.cross ; if format="dlmap" see below |
phefile |
see read.cross ; if format="dlmap" see below |
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 |
type |
Type of experimental cross; only necessary if format="dlmap" or "other"; if not input, will be assumed that data is from unrelated individuals |
step |
Step size for localization stage, i.e. if step=2 , grid
of positions spaced 2 cM apart are considered for QTL locations. If
step=0 (default) positions are only located at markers. |
fixpos |
Alternative to specifying a step size - if fixpos=2 ,
2 evenly spaced positions between each marker are considered as QTL locations.
If fixpos=0 (default) positions are only located at markers. |
estmap |
Flag for whether to re-estimate the linkage map. Cannot be done for format="other" |
... |
additional arguments to read.cross |
This function constructs dlcross
objects for input into
dlmap.asreml
or dlmap.lme
. The format
argument allows for a wide range of input data formats, including all those
compatible with read.cross
. In addition, format="dlmap"
takes three files or objects in the following form.
genfile
: First row contains an identifier variable and marker names.
Following rows contain genotype values for each individual
phefile
: First row contains names of phenotypic and environmental traits. One of these traits must be an identifier for each individual.
Following rows contain values of the traits for each individual. Note: This file may contain more observations than the file containing the marker data
mapfile
: Contains marker names, chromosome groupings and positions
If a single set of trait values is available for each genotype, then
phenotypic data will be input through the arguments genobj
, file
,
or phefile
(depending on the file format).
The argument pheobj
allows for input of phenotypic data on replicates
or additional individuals which are not necessarily genotyped.
Choosing format="other" allows for association mapping populations to be analyzed, and in this case the data can be input as with format="dlmap", but a genetic linkage map is not required. Hence the mapfile only needs the first two columns of marker names and chromosome groupings.
Object with class "dlcross" which can be input to dlmap.asreml or dlmap.lme. Contains the following elements:
dfMerged |
Data frame to be used in dlMapping analysis |
map |
Original genetic map |
nphe |
Number of phenotypic traits |
loc |
A flag for whether to run the localization stage |
idname |
the ID name input to the function |
mapp |
If format is not "other", genetic map augmented by imputed genotypes at grid of positions |
genCross |
if format is not "other", rqtl cross object. CAUTION: if there are replicates, i.e., more phenotypic data than genotypic, this object will not contain all of the phenotypic data for the sample |
Emma Huang and Andrew George
Huang, BE and George, AW. 2009. Look before you leap: A new approach to QTL mapping. TAG 119:899-911
# load dataset data(BSdat) data(BSphe) # convert data to dlmap format dl.in1 <- dlcross(format="rqtl", genobj=BSdat, idname="ID", fixpos=1) # convert data with separate phenotypic trait file dl.in2 <- dlcross(format="rqtl", genobj=BSdat, pheobj=BSphe, idname="ID", step=5)