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.
providing 
.