GGtools (version 5.8.0)

best.trans.eQTLs: collect strongest trans SNP-gene associations in a buffer of size K genes per SNP

Description

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

Usage

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)

Arguments

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.

Value

instance of transManager-class

Examples

## 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)