lfc {IntEREst} | R Documentation

## Log fold change

### Description

Log fold change estimation and normalized log fold change using `edgeR` package.

### Usage

    lfc(x, fcType="edgeR", sampleAnnoCol=c(), sampleAnnotation=c(),
    	silent=TRUE, group=c(), rejection.region="doubletail",
    	pseudoCnt=1, log2=TRUE, ...)

### Arguments

`x` | Object of type `SummarizedExperiment`.
`fcType` | Available as "scaledRetention" or "edgeR" (as default) corresponding to either log fold change of scaled retention values or degeR normalized log fold change values.
`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")`.
`silent` | Whether run `exactTestInterest` silently, without warnings.
`group` | Vector to manually define the sample groups (or annotations). It is ignored if `sampleAnnoCol` is defined.
`rejection.region` | The rejection.region parameter in `exactTest`, considered only if `fcType` is "edgeR".
`pseudoCnt` | Pseudo count for log transformation (default=1).
`log2` | Logical value either TRUE (default) or FALSE indicating whether the foldchanges should be log 2 transformed.
`...` | Other parameter settings from the `exactTestInterest` function.

### Value

Vector including fold change values.

### Author(s)

Ali Oghabian

### See Also

`exactTestInterest`, `u12DensityPlotIntron`

### 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"),
    		health=c("healthy","unhealthy","healthy","unhealthy")
    		, row.names=paste("sam", 1:4, sep="")
    	)
    )

    lfcFpkm<- lfc(InterestResultObj, fcType="scaledRetention",
    	sampleAnnoCol="health",
    	sampleAnnotation=c("unhealthy", "healthy"),
    	silent=TRUE, group=c(), pseudoFpkm=1, log2=TRUE)
    lfcFpkm2<- lfc(InterestResultObj, fcType="scaledRetention",
    	group=c("healthy","unhealthy","healthy","unhealthy"),
    	sampleAnnotation=c("unhealthy", "healthy"),
    	silent=TRUE, pseudoFpkm=1, log2=TRUE)

    lfcEdgeRFpkm<- lfc(InterestResultObj, fcType="edgeR",
    	sampleAnnoCol="health",
    	sampleAnnotation=c("unhealthy", "healthy"),
    	silent=TRUE, group=c(), pseudoFpkm=1, log2=TRUE)

[Package IntEREst version 1.2.2 Index]