GGtools (version 5.8.0)

transScores: obtain the top trans associations for each SNP in an smlSet

Description

obtain the top trans associations for each SNP in an smlSet

Usage

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)

Arguments

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.

Value

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

Examples

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