transScores: obtain the top trans associations for each SNP in an smlSet
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Value Author(s) Examples

obtain the top trans associations for each SNP in an smlSet

transScores( tconfig )

transScores.legacy(smpack, snpchr = "chr1", rhs, K = 20, targdirpref = "tsco", geneApply = lapply, 
  chrnames = paste("chr", as.character(1:22), sep = ""), geneRanges = NULL, snpRanges = NULL, 
  radius = 2e+06, renameChrs = NULL, probesToKeep = NULL, batchsize = 200, 
  genegran = 50, shortfac = 10, wrapperEndo = NULL, 
  geneannopk = "illuminaHumanv1.db", 
  snpannopk = snplocsDefault(), gchrpref = "",
                 schrpref = "ch", exFilter=function(x)x,
   smFilter=function(x)x,
   SSgen=GGBase::getSS)

meta.transScores (smpackvec = c("GGdata", "hmyriB36"),
    snpchr = "22", rhsList=list(~1, ~1), K = 20, targdirpref = "mtsco",
    geneApply = lapply, chrnames = as.character(21:22),
    radius = 2e+06, renameChrs=NULL,
    probesToKeep=NULL, batchsize=200, genegran=50, shortfac=10, wrapperEndo=NULL,
    geneannopk = "illuminaHumanv1.db", snpannopk = snplocsDefault(),
    gchrpref = "", schrpref="ch",
    exFilterList= list(function(x)x, function(x)x),
    SMFilterList = list(function(x)x, function(x)x),
    SSgen = GGBase::getSS)

`tconfig`	instance of `TransConfig-class`
`smpack`	name of package holding eset.rda providing 'ex' ExpressionSet when loaded, and holding SnpMatrix instances in inst/parts
`smpackvec`	vector of names of package holding eset.rda providing 'ex' ExpressionSet when loaded, and holding SnpMatrix instances in inst/parts
`snpchr`	name or vector of chromosome names of SNPs of interest
`rhs`	right hand side of snp.rhs.tests model for which expression is left hand side, e.g., covariates other than genotype
`rhsList`	list of right hand side of snp.rhs.tests model for which expression is left hand side, e.g., covariates other than genotype, one per element of `smpackvec`
`K`	number of most highly associated features to be retained
`targdirpref`	prefix of target folder name (passed to `eqtlTests`
`geneApply`	passed to `eqtlTests`
`chrnames`	names of chromosomes harboring genes that will be tested for association with genotype
`geneRanges`	list of `GRanges-class` instances containing chromosomal coordinate defined regions occupied by genes, with regions partitioned by chromosomes, and list element names as given in `chrnames` above
`snpRanges`	list of `GRanges-class` instances with SNP addresses
`radius`	radius within which an association is considered cis and therefore the corresponding test statistic is set to zero
`renameChrs`	passed to `getSS`
`probesToKeep`	passed to `getSS`
`batchsize`	defines batch size for `ffrowapply`
`genegran`	passed to `eqtlTests`
`shortfac`	passed to `eqtlTests`
`wrapperEndo`	a function accepting and returning an smlSet instance, evaluated before numerical analysis of associations, which will be executed on the output of this function
`gchrpref`	prefix to convert `chrnames` into appropriate tokens for obtaining gene metadata; in future this may need to be a string transformation function
`schrpref`	prefix to convert `chrnames` into appropriate tokens for use with `snplocs` for the SNP location information package identified in `snpannopack` parameter below
`geneannopk`	character string naming a Bioconductor .db expression chip annotation package
`snpannopk`	character string naming a Bioconductor SNPlocs.* SNP metadata package
`exFilter`	function to transform ExpressionSet component of retrieved smlSet, to reduce probe sets in use, for example
`smFilter`	function to transform smlSet instance before use; filter can affect genotypes in smList(x)[[1]], for example
`exFilterList`	list of functions serving as exFilters for each of the elements of smpackvec
`SMFilterList`	list of functions servicing as wrapperEndos for each of the elements of smpackvec
`SSgen`	function to be used to create smlSet instance for testing – in general, GGBase::getSS has been used to pull the ExpressionSet and SnpMatrix data from a named package, but in some cases a specialize task is needed to create the desired smlSet. Whatever is passed to SSgen must return an smlSet instance.

a list with elements

`scores`	an S by K ff matrix where S is number of SNPs, K is number of best features to be retained, with element s,k the kth largest score statistic among association tests computed for SNP s
`inds`	an S by K ff matrix with s,k element telling which element of guniv (see below) is the gene giving the kth largest score statistic for association
`guniv`	the vector of gene identifiers defining the universe of genes tested
`snpnames`	vector of SNP identifiers
`call`	the call used to create the result

VJ Carey <stvjc@channing.harvard.edu>

## Not run: 
library(GGdata)
# need to define the geneRanges and snpRanges ...
transScores("GGdata", "20", renameChrs="chr20", chrnames="chr21")

## End(Not run)