read.cross {qtl} | R Documentation |
Data for a QTL experiment is read from a set of files and converted
into an object of class 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","N/A","na","n/a"," "), genotypes=c("A","H","B","D","C"), estimate.map=TRUE, dec=".", quote="\"'")
format |
Specifies the format of the data. |
dir |
Directory in which the data files will be found. In
Windows, use forward slashes ("/" ) or double backslashes
("\\" ) to specify directory trees. |
file |
The main imput file for formats csv and mm . |
genfile |
File with genotype data (formats karl and
gary only). |
mapfile |
File with marker position information (all formats
except csv ). |
phefile |
File with phenotype data (formats karl and
gary only). |
chridfile |
File with chromosome ID for each marker (gary
format only). |
mnamesfile |
File with marker names (gary format only). |
pnamesfile |
File with phenotype names (gary format
only). |
sep |
The field separator (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. |
na.strings |
A vector of strings which are to be interpreted as
missing values (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. |
genotypes |
A vector of character strings specifying the genotype
codes (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: Pay
careful attention to the third and fourth of these; the order of
these can be confusing! These five character strings are converted
to (1,2,3,5,4) in the cross object that is returned. |
estimate.map |
For formats 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
est.map . |
dec |
see read.table (base) . |
quote |
see read.table (base) . |
The available formats are comma-delimited (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.
An object of class cross
, which is a list with two components:
geno |
This is a list with elements corresponding to
chromosomes. 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. |
pheno |
data.frame of size (n.ind x n.phe ) containing the
phenotypes. |
The genotypes for the X chromosome require special care!
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.
The input file is a text file with a specified field delimiter
(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.
This format requires two files. The so-called rawfile, specified by
the argument file
, contains the genotype and phenotype
data. Rows beginning with the symbol #
are ignored. The first
line should be either data type f2 intercross
or
data type f2 backcross
. The second line should begin with
three numbers indicating the numbers of individuals, markers and
phenotypes in the file. This line may include the word symbols
followed by symbol assignments (see the documentation for mapmaker,
and cross your fingers). The rest of the lines give genotype data
followed by phenotype data, with marker and phenotype names always
beginning with the symbol *
.
A second file contains the genetic map information, specified with
the argument mapfile
. (For the Mapmaker format, if
genfile
is specified but not mapfile
, we assume that
genfile
is the file to use.) The map file may be in
one of two formats. The function will determine which format of map
file is presented.
The simplest format for the map file is not standard for the Mapmaker software, but is easy to create. The file contains two or three columns separated by white space and with no header row. The first column gives the chromosome assignments. The second column gives the marker names, with markers listed in the order along the chromosomes. An optional third column lists the map positions of the markers.
Another possible format for the map file is the .maps
format, which is produced by Mapmaker. The code for reading this
format was written by Brian Yandell; I'm not really familiar with it
myself.
Marker order is taken from the map file, either by the order they are presented or by the cM positions, if specified.
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.
This format requires a single file (that produced by the Map Manager QTX program).
This format requires two files: the .cro
and .map
files
for the QTL Cartographer (produced by the QTL Cartographer
sub-program, Rmap and Rcross).
Note that the QTL Cartographer cross types are converted as follows: RF1 to riself, RF2 to risib, RF0 (doubled haploids) to bc, B1 or B2 to bc, RF2 or SF2 to f2.
This format requires the six files. All files have default names, and so the file names need not be specified if the default names are used.
genfile
(default = "geno.dat"
) contains the genotype
data. The file contains one line per individual, with genotypes for
the set of markers separated by white space. Missing values are
coded as 9, and genotypes are coded as 0/1/2 for AA/AB/BB.
mapfile
(default = "markerpos.txt"
) contains two
columns with no header row: the marker names in the first column and
their cM position in the second column. If marker positions are not
available, use mapfile=TRUE
, and a dummy map will be inserted.
phefile
(default = "pheno.dat"
) contains the phenotype
data, with one row for each mouse and one column for each phenotype.
There should be no header row, and missing values are coded as
"-"
.
chridfile
(default = "chrid.dat"
) contains the
chromosome identifier for each marker.
mnamesfile
(default = "mnames.txt"
) contains the marker
names.
pnamesfile
(default = "pnames.txt"
) contains the names
of the phenotypes. If phenotype names file is not available, use
pnamesfile=NULL
; arbitrary phenotype names will then be
assigned.
This format requires three files; all files have default names, and so need not be specified if the default name is used.
genfile
(default = "gen.txt"
) contains the genotype
data. The file contains one line per individual, with genotypes
separated by white space. Missing values are coded 0; genotypes are
coded as 1/2/3/4/5 for AA/AB/BB/not BB/not AA.
mapfile
(default = "map.txt"
) contains the map
information, in the following complicated format:
n.chr
n.mar(1) rf(1,1) rf(1,2) ... rf(1,n.mar(1)-1)
mar.name(1,1)
mar.name(1,2)
...
mar.name(1,n.mar(1))
n.mar(2)
...
etc.
phefile
(default = "phe.txt"
) contains a matrix of
phenotypes, with one individual per line. The first line in the
file should give the phenotype names.
Karl W Broman, kbroman@jhsph.edu; Brian S. Yandell
write.cross
, sim.cross
;
the sampledata
directory in the package distribution contains
sample data files in all formats except Gary's.
## Not run: # comma-delimited format dat1 <- read.cross("csv", dir="Mydata", file="mydata.csv") # Mapmaker format dat2 <- read.cross("mm", dir="Mydata", file="mydata.raw", mapfile="mydata.map") # Map Manager QTX format dat3 <- read.cross("qtx", dir="Mydata", file="mydata.qtx") # QTL Cartographer format dat4 <- read.cross("qtlcart", dir="Mydata", file="qtlcart.cro", mapfile="qtlcart.map") # Gary format dat5 <- read.cross("gary", dir="Mydata", genfile="geno.dat", mapfile="markerpos.txt", phefile="pheno.dat", chridfile="chrid.dat", mnamesfile="mnames.txt", pnamesfile="pnames.txt") # Karl format dat6 <- read.cross("karl", dir="Mydata", genfile="gen.txt", phefile="phe.txt", mapfile="map.txt")## End(Not run)