testUsage {InPAS} | R Documentation

## do test for dPDUI

### Description

do test for dPDUI

### Usage

    testUsage(CPsites, coverage, genome, utr3, BPPARAM=NULL,
              method=c("limma", "fisher.exact",
                        "singleSample", "singleGroup"),
              normalize=c("none", "quantiles", "quantiles.robust",
                            "mean", "median"),
              design, contrast.matrix, coef=1, robust=FALSE, ...,
              gp1, gp2)

### Arguments

`CPsites` | outputs of CPsites
`coverage` | coverage for each sample, outputs of coverageFromBedGraph
`genome` | an object of BSgenome
`utr3` | output of utr3Annotation
`BPPARAM` | An optional `BiocParallelParam` instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply.
`method` | test method. see `singleSampleAnalyze`,`singleGroupAnalyze`, `fisher.exact.test`,`limmaAnalyze`
`normalize` | normalization method
`design` | the design matrix of the experiment, with rows corresponding to arrays and columns to coefficients to be estimated. Defaults to the unit vector meaning that the arrays are treated as replicates. see model.matrix
`contrast.matrix` | numeric matrix with rows corresponding to coefficients in fit and columns containing contrasts. May be a vector if there is only one contrast. see makeContrasts
`coef` | column number or column name specifying which coefficient or contrast of the linear model is of interest. see more topTable. default value: 1
`robust` | logical, should the estimation of the empirical Bayes prior parameters be robustified against outlier sample variances?
`...` | other arguments are passed to lmFit.
`gp1` | tag names involved in group 1
`gp2` | tag names involved in group 2

### Details

if method is "limma", design matrix and contrast is required. if method is "fisher.exact", gp1 and gp2 is required.

### Value

a list with test results. the output of test results is a matrix.

### Author(s)

Jianhong Ou

### See Also

`singleSampleAnalyze`,`singleGroupAnalyze`, `fisher.exact.test`,`limmaAnalyze`

### Examples

        library(limma)
        path <- file.path(find.package("InPAS"), "extdata")
        load(file.path(path, "CPs.MAQC.rda"))
        load(file.path(path, "coverage.MAQC.rda"))
        library(BSgenome.Hsapiens.UCSC.hg19)
        data(utr3.hg19)
        tags <- names(coverage)
        g <- factor(gsub("\\..*$", "", tags))
        design <- model.matrix(~-1+g)
        colnames(design) <- c("Brain", "UHR")
        contrast.matrix<-makeContrasts(contrasts="Brain-UHR",levels=design)
        res <- testUsage(CPsites=CPs,
                     coverage=coverage,
                     genome=BSgenome.Hsapiens.UCSC.hg19,
                     utr3=utr3.hg19,
                     method="limma",
                     design=design,
                     contrast.matrix=contrast.matrix)

[Package InPAS version 1.20.0 Index]