exactTestInterest {IntEREst} | R Documentation

## Exact test

### Description

Compute genewise exact test between two groups of read counts, using the `edgeR` package.

### Usage

    exactTestInterest(x, sampleAnnoCol=c(), sampleAnnotation=c(),
    	geneIdCol, silent=TRUE, group=c(), rejection.region="doubletail",
    	big.count=900, prior.count=0.125, disp="common", ...)

### Arguments

`x` | Object of type `SummarizedExperiment`.
`sampleAnnoCol` | Which colummn of `colData` of `x` to consider for the analysis.
`sampleAnnotation` | A vector of size 2 which cotains values from `colData` of `SummarizedExperiment` object; e.g. if `getAnnotation(x)[, sampleAnnoCol]= c("test", "test", "ctrl","ctrl", ...)` , and the goal is to compare "test" and "ctrl" samples, `sampleAnnotation` should either be `c("test", "ctrl")` or `c("ctrl", "test")`.
`geneIdCol` | Column name (or number of column) in `rowData` of `x`, i.e. `SummarizedExperiment` object, that represents the gene ID of the introns and exons in `x`.
`silent` | Whether run the function silently, i.e. without printing the top differential expression tags.
`group` | Vector to manually define the sample groups (or annotations). It is ignored if `sampleAnnopCol` is defined.
`rejection.region` | The `rejection.region` parameter in `exactTest` from `edgeR` package.
`big.count` | The `big.count` parameter in `exactTest` from `edgeR` package.
`prior.count` | The `prior.count` parameter in `exactTest` from `edgeR` package.
`disp` | The type of estimating the dispersion in the data. Available options are: "tagwise", "trended", "common" and "genewise". It is also possible to assign a number for manually setting the `disp`.
`...` | Other parameter settings for the `estimateDisp` function (e.g. the `design` parameter) in the `edgeR` package.

### Value

`table` | Data frame containing columns for the log2 fold-change (logFC), the average of log2 counts-per-million (logCPM), and the two-sided p-value (PValue).
`comparison` | The name of the two compared groups.
`dispersionType` | The name of the type of dispersion used.
`dispersion` | The estimated dispersion values.

### Author(s)

Ali Oghabian

### See Also

`lfc`, `glmInterest`, `qlfInterest`, `treatInterest`, `DEXSeqIntEREst`

### Examples

    geneId<- paste("gene", c(rep(1,5), rep(2,5), rep(3,5), rep(4,5)),
    	sep="_")
    readCnt1<- sample(1:100, 20)
    readCnt2<- sample(1:100, 20)
    readCnt3<- sample(1:100, 20)
    readCnt4<- sample(1:100, 20)
    fpkm1<- readCnt1/(tapply(readCnt1, geneId, sum))[geneId]
    fpkm2<- readCnt2/(tapply(readCnt2, geneId, sum))[geneId]
    fpkm3<- readCnt3/(tapply(readCnt3, geneId, sum))[geneId]
    fpkm4<- readCnt4/(tapply(readCnt4, geneId, sum))[geneId]

    # Creating object using test data
    interestDat<- data.frame(
    		int_ex=rep(c(rep(c("exon","intron"),2),"exon"),4),
    		int_ex_num= rep(c(1,1,2,2,3),4),
    		gene_id= geneId,
    		sam1_readCnt=readCnt1,
    		sam2_readCnt=readCnt2,
    		sam3_readCnt=readCnt3,
    		sam4_readCnt=readCnt4,
    		sam1_fpkm=fpkm1,
    		sam2_fpkm=fpkm2,
    		sam3_fpkm=fpkm3,
    		sam4_fpkm=fpkm4
    )
    readFreqColIndex<- grep("_readCnt$",colnames(interestDat))
    scaledRetentionColIndex<- grep("_fpkm$",colnames(interestDat))

    scalRetTmp<- as.matrix(interestDat[ ,scaledRetentionColIndex])
    colnames(scalRetTmp)<-gsub("_fpkm$","", colnames(scalRetTmp))

    frqTmp<- as.matrix(interestDat[ ,readFreqColIndex])
    colnames(frqTmp)<-gsub("_readCnt$","", colnames(frqTmp))

    InterestResultObj<- InterestResult(
    	resultFiles=paste("file",1:4, sep="_"),
    	rowData= interestDat[ , -c(readFreqColIndex,
    		scaledRetentionColIndex)],
    	counts= frqTmp,
    	scaledRetention= scalRetTmp,
    	scaleLength=TRUE,
    	scaleFragment=FALSE,
    	sampleAnnotation=data.frame(
    		sampleName=paste("sam",1:4, sep=""),
    		gender=c("M","M","F","F"), row.names=paste("sam", 1:4, sep="")
    	)
    )

    res<- exactTestInterest(InterestResultObj, sampleAnnoCol="gender",
    	sampleAnnotation=c("F","M"), geneIdCol= "gene_id",
    	silent=TRUE, disp="common")

[Package IntEREst version 1.10.2 Index]