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]