snpScreen {GGtools} | R Documentation

## compute model fits over a sequence of SNPs

### Description

compute model fits over a sequence of SNPs

### Usage

    snpScreen(racExSet, snpMeta, gene, formTemplate, fitter, gran, ...)
    extract_p(ssr)
    plot_mlp(ssr, snpMeta, gchr=NULL, geneLocDF=NULL, ps = NULL, pch = 20, cex = 0.5, local=FALSE,
      plotf=smoothScatter, organism="human")

### Arguments

`racExSet` | instance of `racExSet-class`
`snpMeta` | instance of `snpMeta-class`
`gene` | instance of `genesym-class` class identifying the expression phenotype to be regarded as dependent variable
`gchr` | string stating chromosome on which gene is resident; looked up in geneLocDF if not supplied
`geneLocDF` | data frame that has one row for each gene symbol, in column `gene', and the chromosome on which it lives, in column `chr'
`formTemplate` | a formula having form `~.` or `~factor(.)`, literally, to specify additive or nonadditive models for effects of rare allele copy number
`fitter` | R fitting function that can work with formulas and data frames, for example `lm`, or, if not a fitting function, a special object in the package, either `fastHETfitter`, or `fastAGMfitter`, see details below
`gran` | a numeric convenience parameter; if not 1, SNPs will be deterministically selected with frequency 1/`gran` along the linear sequence in the racExSet racAssay structure
`...` | ... – not in use
`ssr` | `snpScreenResult` instance
`ps` | a string with a probe set identifier
`pch` | for passage to `scatterSmooth`
`cex` | for passage to `scatterSmooth`
`local` | by default (local==FALSE) the plot is made over the entire chromosome; if local==TRUE, the plot is made over the segment of the chromosome within which the snps screened lie; this only makes a difference if the racExSet used in the screen has been SNP-filtered relative to the HapMap SNP set.
`plotf` | function to use for rendering – with really high-density genotyping, the default works well; in sparse cases, use `plot`.
`organism` | string used for plot annotation

### Details

for snpScreen: If `options()$verbose == TRUE` then every 100th index in the vector of snps is printed to stdout to show rate of progress.

`snpScreenResult` is a container for relevant information about a screen, including a list of fit objects.

For result processing, many SNPs have no variation in observed samples and statistical tests of association are indeterminate. NAs will be returned for tests on such SNPs.

`fastAGMfitter` is an object that wraps a call to a C routine for simple least square fitting of an additive genetic model. `fastHETfitter` will call C code that compares heterozygous to homozygous.

`plot_mlp` returns a list of x and y values for the plotted points.

### Value

creates a list of model fit results; `try` is used to allow failure of fit (e.g., `lm` may fail if a singular model matrix is computed

### Author(s)

Vince Carey <stvjc@channing.harvard.edu>

### Examples

    example(make_racExSet)
    dem
    dem = exclMono(dem)
    snpNames(dem)[1:4]
    featureNames(dem)[1:4]
    data(chr20GGdem)
    data(chr20meta)
    data(geneLocs_hsa)
    scr1 = snpScreen(dem, chr20meta, genesym("DDR1"), ~., lm,  gran=100 )
    scr1[[1]]
    scr2 = snpScreen(dem, chr20meta, genesym("DDR1"), ~factor(.), lm,  gran=200 )
    scr2[[1]]
    plot_mlp(scr1, chr20meta, geneLocDF=geneLocs_hsa)
    chr20GGdem = exclMono(chr20GGdem)
    ut = unix.time(scr2 <- snpScreen(chr20GGdem, chr20meta, genesym("CPNE1"), ~., fastAGMfitter))
    ut
    scr2
    plot_mlp(scr2, chr20meta, geneLocDF=geneLocs_hsa)
    #
    # here we work on a WebQTL computation
    #
    # get the expr+genotype data
    data(gse2031GG)
    # get a provisional snp metadata structure
    data(INB34snpMeta)
    # run a screen for Erdr1
    ss = snpScreen(gse2031GG, INB34snpMeta, genesym("Erdr1"), ~., fastAGMfitter)
    plot_mlp(ss, INB34snpMeta, gchr="all", plotf=plot, organism="mouse" )

[Package GGtools version 1.6.1 Index]