Strains2rac {GGtools} | R Documentation

## convert a Wellcome 'Strains' genotyping file to rare allele count form

### Description

convert a Wellcome 'Strains' genotyping file to rare allele count form, or create a racExSet using such a file

### Usage

    Strains2rac(strfile)
    INBREDSworkflow(inbfile, emat, estrains, pd, mi, anno, fixup= NULL, fixchr =
         function(x) gsub("_random", "", x))

### Arguments

`strfile` | name of the text file to be converted
`inbfile` | name of the text file to be converted
`emat` | matrix of expression data
`estrains` | character vector of strains corresponding to columns of `emat`
`pd` | `AnnotatedDataFrame-class` instance for `emat`
`mi` | `MIAME-class` instance
`anno` | character string for annotation environment package
`fixup` | transformation from columns of strain genotype file `strfile` to `estrains` tokens, if necessary
`fixchr` | modify the chromosome tags if necessary

### Details

### Value

`Strains2rac` creates a list with genotype matrix, chr and pos
`INBREDSworkflow` creates a list with components `racExSet` and `snpMetaWhole` (because the INBREDS files are whole-genome, not chromosome specific)

### Note

See the commented example for build 34 Wellcome Inbreds file for BXD strains, `INB34snpMeta`.

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

### References

### See Also

### Examples

    fi = system.file("fileDemos/StrainInit.txt", package="GGtools")
    dem = Strains2rac(fi)
    names(dem)
    dim(dem[[1]])
    data(gse2031GG)
    fixbxd = function(x) {
    # because such various labels are used in the INBREDS file
     gsub("BXD\\.", "BXD", gsub(".Ty", "", gsub(".TyJ", "", x)))
    }
    INBREDSworkflow( fi, exprs(gse2031GG), as.character(gse2031GG$str),
            phenoData(gse2031GG), new("MIAME"), "mgu74av2", fixbxd )
    #
    # the real INB34snpMeta structure is built by
    # fixchr = function(x) gsub("_random", "", x)
    #INBREDSworkflow( "Strains-0.09052005.txt", exprs(gse2031GG), as.character(gse2031GG$str),
    #       phenoData(gse2031GG), new("MIAME"), "mgu74av2", fixbxd, fixchr )

[Package GGtools version 1.4.0 Index]