gwSnpTests {GGtools} | R Documentation |
methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests(sym, sms, cnum, ...)
sym |
genesym, probeId, or formula instance |
sms |
smlSet instance |
cnum |
chrnum instance or missing |
... |
... |
invokes snpMatrix test procedures as appropriate
gwSnpScreen is deprecated and simply throws a message indicating this.
gwSnpScreenResult or cwSnpScreenResult instance
Vince Carey <stvjc@channing.harvard.edu>
if (!exists("hmceuB36.2021")) data(hmceuB36.2021) # condense to founders only hmFou = hmceuB36.2021[, which(hmceuB36.2021$isFounder)] # show basic formula fit f1 = gwSnpTests(genesym("CPNE1")~male, hmFou, chrnum(20)) f1 plot(f1) # show how to avoid adjusted fit f1b = gwSnpTests(genesym("CPNE1")~1-1, hmFou, chrnum(20)) # show gene set modeling on chromosome library(GSEABase) gs1 = GeneSet(c("CPNE1", "ADA")) geneIdType(gs1) = SymbolIdentifier() f2 = gwSnpTests(gs1~male, hmFou, chrnum(20)) f2 names(f2) plot(f2[["ADA"]]) # show 'smlSet-wide' fit f3 = gwSnpTests(gs1~male, hmFou) f3