cross. The comma-delimited format
(csv) is recommended. All formats require chromosome
assignments for the genetic markers, and assume that markers are in
their correct order.read.cross(format=c("csv","mm","qtx","qtlcart","gary","karl"), dir="",
file, genfile, mapfile, phefile, chridfile, mnamesfile,
pnamesfile, sep=",", na.strings=c("-","NA"),
genotypes=c("A","H","B","D","C"), estimate.map=TRUE)"/") or double backslashes
("\\") to specify directory trees.csv and mm.karl and
gary only).csv).karl and
gary only).gary
format only).gary format only).gary format
only).csv format only). This is
generally ",", but could be any other character (such as
"\t" for tab), as long as that character does not appear in
any of the records.csv format only). These are interpreted
globally for the entire file, so missing value codes in phenotypes
must not be valid genotypes, and vice versa.csv format only). Generally this is a vector of
length 5, with the elements corresponding to AA, AB, BB, not AA
(i.e., AB or BB), and not BB (ie, AB or BB). Note<csv, qtx, mm, and
gary only: if TRUE and marker positions are not included in
the input files, the genetic map is estimated using the function
cross, which is a list with two components:names(geno) contains the names of the
chromsomes. Each chromosome is itself a list, and is given class
A or X according to whether it is autosomal
or the X chromosome.
There are two components for each chromosome: data, a matrix
whose rows are individuals and whose columns are markers, and
map, either a vector of marker positions (in cM) or a matrix
of dim (2 x n.mar) where the rows correspond to marker
positions in female and male genetic distance, respectively.
The genotype data for a backcross is coded as follows: NA = missing,
1 = AA, 2 = AB.
For an F2 intercross, the coding is NA = missing, 1 = AA, 2 = AB, 3
= BB, 4 = not BB (ie AA or AB; D in mapmaker/qtl), 5 = not AA (ie AB
or BB; C in mapmaker/qtl).
For a 4-way cross, the mother and father are assumed to have
genotypes AB and CD, respectively. The genotype data for the
progeny is assumed to be phase-known, with the following coding
scheme: NA = missing, 1 = AC, 2 = BC, 3 = AD, 4 = BD, 5 = A = AC or AD,
6 = B = BC or BD, 7 = C = AC or BC, 8 = D = AD or BD, 9 = AC or BD,
10 = AD or BC.n.ind x n.phe) containing the
phenotypes.Any X chromosome genotype data should be coded like an autosome in a backcross, with genotypes A and H.
The phenotype data should contain a column named "sex" which indicates the sex of each individual, either coded as 0=female and 1=male, or as a factor with levels female/male or f/m. Case will be ignored both in the name and in the factor levels. If no such phenotype column is included, it will be assumed that all individuals are of the same sex.
In the case of an intercross, the phenotype data may also contain a column names "pgm" (for "paternal grandmother") indicating the direction of the cross. It should be coded as 0/1 with 0 indicating the cross (AxB)x(AxB) or (BxA)x(AxB) and 1 indicating the cross (AxB)x(BxA) or (BxA)x(BxA). If no such phenotype column is included, it will be assumed that all individuals come from the same direction of cross.
In a backcross, females should be coded 1=AA and 2=AB, while males should be coded 1=A and 2=B (hemizygous).
In an intercross, males should be coded as 1=A and 2=B (hemizygous), which females should be coded as 1=AA and 2=AB for pgm=0, and 1=BB and 2=AB for pgm=1.
sep) (a comma is recommended).The first line should contain the phenotype names followed by the marker names. At least one phenotype must be included; for example, include a numerical index for each individual.
The second line should contain blanks in the phenotype columns,
followed by chromosome identifiers for each marker in all other
columns. If a chromosome has the identifier X or x, it
is assumed to be the X chromosome; otherwise, it is assumed to be an
autosome.
An optional third line should contain blanks in the phenotype columns, followed by marker positions, in cM.
Marker order is taken from the cM positions, if provided; otherwise, it is taken from the column order.
Subsequent lines should give the data, with one line for each individual, and with phenotypes followed by genotypes. If possible, phenotypes are made numeric; otherwise they are converted to factors.
The cross is determined to be a backcross if only the first two elements
of the genotypes string are found; otherwise, it is assumed to
be an intercross.
csv), Mapmaker
(mm), Map Manager QTX (qtx), Gary Churchill's format
(gary) and Karl Broman's format (karl). The required
files and their specification for each format appears below. The
comma-delimited format is recommended. Note that these formats work
only for backcross and intercross data.