read.cross {qtl}R Documentation

Read data for a QTL experiment

Description

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.

Usage

read.cross(format=c("csv","mm","qtx","qtlcart","gary","karl"), dir="",
           file, genfile, mapfile, phefile, chridfile, mnamesfile,
           pnamesfile, na.strings=c("-","NA"),
           genotypes=c("A","H","B","D","C"), estimate.map=TRUE,
           convertXdata=TRUE, ...)

Arguments

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).
na.strings A vector of strings which are to be interpreted as missing values (csv format and gary only). For the csv format, these are interpreted globally for the entire file, so missing value codes in phenotypes must not be valid genotypes, and vice versa. For the gary format, these are used only for the phenotype data.
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.
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.
convertXdata If TRUE, any X chromosome genotype data is converted to the internal standard, using columns sex and pgm in the phenotype data if they available or by inference if they are not. If FALSE, the X chromsome data is read as is.
... Additional arguments, passed to the function read.table in the case that format="csv". In particular, one may use the argument sep to specify the field separator (the default is a comma) and dec to specify the character used for the decimal point (the default is a period).

Details

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.

Value

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.

X chromosome

The genotypes for the X chromosome require special care!

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.

The internal storage of X chromosome data is quite different from that of autosomal data. Males are coded 1=AA and 2=BB; females with pgm==0 are coded 1=AA and 2=AB; and females with pgm==1 are coded 1=BB and 2=AB. If the argument convertXdata is TRUE, conversion to this format is made automatically; if FALSE, no conversion is done, summary.cross will likely return a warning, and most analyses will not work properly.

CSV format

The input file is a comma-delimited text file (a different field separator may be specified via the argument sep which will be passed to the function read.table).

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.

Mapmaker format

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.

Map Manager QTX format

This format requires a single file (that produced by the Map Manager QTX program).

QTL Cartographer format

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.

Gary format

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.

Karl format

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.

Author(s)

Karl W Broman, kbroman@jhsph.edu; Brian S. Yandell

See Also

write.cross, sim.cross; the sampledata directory in the package distribution contains sample data files in all formats except Gary's.

Examples

## 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)

[Package qtl version 0.98-57 Index]