best.trans.eQTLs: collect strongest trans SNP-gene associations in a buffer of...
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Value Author(s) Examples

collect strongest trans SNP-gene associations in a buffer of size K genes per SNP

best.trans.eQTLs(smpack, rhs, genechrnum, snpchrnum, K = 20, 
   targdirpref = "tsco", batchsize = 200, radius = 2e+06, genequeryprefix = "", 
   snploadprefix = "chr", snplocprefix = "chr", geneannopk, snpannopk, 
   exFilter = function(x) x, smFilter = function(x) x, 
   geneApply = lapply, SSgen = GGBase::getSS)

`smpack`	character string naming a package from which `smlSet-class` instances can be generated using `getSS`
`rhs`	passed to `snp.rhs.tests` for covariate or stratification adjustments; for permutation analysis, covariates should be handled via `regressOut`
`genechrnum`	character vector of chromosome identifiers for genes, typically `as.character(1:22)` for somatic genes in human studies
`snpchrnum`	specific chromosome identifier for all SNP to be analyzed
`K`	the size of the buffer: scores will be recorded for the most strongly associated K genes for each SNP
`targdirpref`	character string where buffer data will be held in ff archives
`batchsize`	passed to `ffrowapply` as scores are filtered from comprehensive testing to fill the buffer
`radius`	numeric: for same-chromosome tests, tests will not be performed for SNP-gene combinations with base-pair proximity smaller than radius
`genequeryprefix`	string: used when the numeric chromosome identifier requires a prefix like ‘chr’ for annotation query resolution on gene location
`snploadprefix`	string: used when the package identified in `smpack` requires a prefix to the `snpchrnum` token for `getSS` retrieval of `smlSet` instance
`snplocprefix`	string: used when the numeric chromosome identifier requires a prefix like ‘chr’ for annotation query resolution on SNP location
`geneannopk`	package to be used for CHRLOC and CHRLOCEND queries for genes
`snpannopk`	package to be used to resolve `snplocs` calls
`exFilter`	function returning an smlSet instance, operating on expression component prior to smFilter application and eQTL testing
`smFilter`	function returning an smlSet instance, operating on the full smlSet
`geneApply`	lapply-like function, typically mclapply or the like
`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.

instance of transManager-class

VJ Carey <stvjc@channing.harvard.edu>

## Not run: 
if (.Platform$OS.type != "windows") {  # ff overwrites failing 5.IX.12
  nsFilter2 = function(sms, var.cutoff=.5) {
   alliq = apply(exprs(sms),1,IQR)
   qs = quantile(alliq,var.cutoff, na.rm=TRUE)
   sms[ which(alliq > qs), ]
  }
  thefilt = function(x) GTFfilter( nsFilter2 (clipPCs(x, 1:10), var.cutoff=.95 ), lower=.05 )
  tfile = tempfile()
  tfold = dir.create(tfile)
  t1 = best.trans.eQTLs( "GGdata", ~1, as.character(20:22), "22",
          geneannopk="illuminaHumanv1.db", snpannopk= snplocsDefault(),
          smFilter=thefilt, snploadprefix="", snplocprefix="ch", targdirpref=tfile)
  tt1 = transTab(t1)
  tt1o = tt1[ order(tt1[,"sumchisq"], decreasing=TRUE), ][1:10,]
  tt1o
  }

## End(Not run)