gwSnpTests {GGtools}R Documentation

methods for iterating association tests (expression vs SNP) across genomes or chromosomes

Description

methods for iterating association tests (expression vs SNP) across genomes or chromosomes

Usage

gwSnpTests(sym, sms, cnum, ...)

Arguments

sym genesym, probeId, or formula instance
sms smlSet instance
cnum chrnum instance or missing
... ...

Details

invokes snpMatrix test procedures as appropriate

gwSnpScreen is deprecated and simply throws a message indicating this.

Value

gwSnpScreenResult or cwSnpScreenResult instance

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

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

[Package GGtools version 3.0.0 Index]