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]