R: Read data for 4- or 8-way RIL

readMWril {qtl} | R Documentation

## Read data for 4- or 8-way RIL

### Description

Data for a set of 4- or 8-way recombinant inbred lines (RIL) is read from a pair of comma-delimited files and converted into an object of class `cross`. We require chromosome assignments for the genetic markers, and assume that markers are in their correct order.

### Usage

    readMWril(dir="", rilfile, founderfile,
              type=c("ri4self", "ri4sib", "ri8self", "ri8selfIRIP1", "ri8sib", "bgmagic16"),
              na.strings=c("-","NA"), rotate=FALSE, ...)

### Arguments

`dir` | Directory in which the data files will be found. In Windows, use forward slashes (`"/"`) or double backslashes (`"\\"`) to specify directory trees.
`rilfile` | Comma-delimited file for the RIL, in the `"csv"` format described in the help file for `read.cross`.
`founderfile` | File with founder strains' genotypes, in the same orientation as the `rilfile`, but with just marker names and the founders' marker genotypes.
`type` | The type of RIL.
`na.strings` | A vector of strings which are to be interpreted as missing values. For the `csv` formats, 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.
`rotate` | If TRUE, the `rilfile` and `founderfile` are rotated (really transposed), with rows corresponding to markers and columns corresponding to individuals.
`...` | Additional arguments, passed to the function `read.table` in the case of `csv` and `csvr` formats. 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 `rilfile` should include a phenotype `cross` containing character strings of the form `ABCDEFGH`, indicating the cross used to generate each RIL. The genotypes should be coded as integers (e.g., 1 and 2).

The founder strains in the `founderfile` should be the strains `A`, `B`, `C`, ..., as indicated in the `cross` phenotype.

The default arrangement of the files is to have markers as columns and individuals/founders as rows. If `rotate=TRUE`, do the opposite: markers as rows and individuals/founders as columns.

### Value

An object of class `cross`; see the help file for `read.cross` for details.

An additional component `crosses` is included; this is a matrix indicating the crosses used to generate the RIL.

### Author(s)

Karl W Broman, broman@wisc.edu

### See Also

`read.cross`, `sim.cross`

### Examples

    ## Not run:
    ril <- read.cross("../Data", "ril_data.csv", "founder_geno.csv", "ri4self",
                      rotate=TRUE)
    ## End(Not run)

[Package qtl version 1.46-2 Index]