| gwSnpTests {GGtools} | R Documentation |
methods for iterating association tests (expression vs SNP) across genomes or chromosomes
gwSnpTests(sym, sms, cnum, cs, ...)
sym |
genesym, probeId, or formula instance |
sms |
smlSet instance |
cnum |
chrnum instance or missing |
cs |
chunksize specification |
... |
... |
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.
gwSnpScreenResult-class or
cwSnpScreenResult-class 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
# 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)