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]