testUsage: do test for dPDUI

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

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)

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.