a vector of candidate package names (potential
smpack arguments to getSS for metaanalysis
across populations or tissues
smchr
the chromosome name as used in the names of the smList output for
the getSS result
obj
an instance of mcwBestCis-class generated using the
package named in smpack
usemaxMAF
if TRUE, label a SNP with maximum MAF observed across
populations, otherwise compute the MAF for the combined genotypes across
populations represented by the various smlSet instances generated with
the smpackvec spec.
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.
Details
computes the MAF of most highly associated SNP per gene, and distance between
that SNP and the transcription limits of the gene, assigning 0 for this if the
SNP lies within the transcription limits
Value
a GRanges instance
Note
This will be used to stratify the permuted scores.