cisSnpTests {GGtools} | R Documentation |
perform tests for eQTL cis to specified genes
cisSnpTests(fmla, smls, radius, ...)
fmla |
standard formula. LHS can be a GeneSet with AnnotationIdentifier
geneIdType. RHS can be predictor formula component using variables
in pData of smls
|
smls |
instance of smlSet |
radius |
numeric value: number of bases up and downstream from probe CHRLOC to be examined for SNP |
... |
not in use |
a list of cwSnpScreen instances
Getting SNP locations is slow for the first event while metadata are brought into scope. Subsequent calls are faster.
VJ Carey <stvjc@channing.harvard.edu>
library(GSEABase) # two genes on chr 20 gs1 = GeneSet(c("CPNE1", "ADA"), geneIdType = SymbolIdentifier()) gs2 = gs1 organism(gs2) = "Homo sapiens" geneIdType(gs2) = AnnotationIdentifier("illuminaHumanv1.db") if (!exists("hmceuB36.2021")) data(hmceuB36.2021) cc = cisSnpTests(gs2~male, hmceuB36.2021, radius=1e5) lapply(cc, function(x) length(p.value(x@.Data[[1]]))) cc = cisSnpTests(gs2~male, hmceuB36.2021, radius=1e6) lapply(cc, function(x) length(p.value(x@.Data[[1]])))