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, cs, ...)

Arguments

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

Details

invokes snpMatrix package test procedures (e.g., snp.rhs.tests as appropriate

chunksize can be specified to divide task up into chunks of chromosomes; gc() will be run between each chunk – this may lead to some benefits when memory capacity is exceeded

The dependent variable in the formula can have class genesym (chip annotation package used for lookup), probeId (direct specification using chip annotation vocabulary), or phenoVar (here we use a phenoData variable as dependent variable). If you want to put expression values on the right-hand side of the model, add them to the phenoData and enter them in the formula.

Value

gwSnpScreenResult-class or cwSnpScreenResult-class 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
# now use a phenoVar
f3b = gwSnpTests(phenoVar("persid")~male, hmFou, chrnum(20))
topSnps(f3b)
## Not run: 
# in example() we run into a problem with sys.call(2); works
# in interpreter
f4 = gwSnpTests(gs1~male, hmFou, snpdepth(250), chunksize(1))
f4
  
## End(Not run)

[Package GGtools version 3.2.0 Index]