transScores {GGtools} | R Documentation |
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 |
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 |
K |
number of most highly associated features to be retained |
targdirpref |
prefix of target folder name (passed to |
geneApply |
passed to |
chrnames |
names of chromosomes harboring genes that will be tested for association with genotype |
geneRanges |
list of |
snpRanges |
list of |
radius |
radius within which an association is considered cis and therefore the corresponding test statistic is set to zero |
renameChrs |
passed to |
probesToKeep |
passed to |
batchsize |
defines batch size for |
genegran |
passed to |
shortfac |
passed to |
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 |
schrpref |
prefix to convert |
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)