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

    lfcFpkm<- lfc(mdsChr22Obj, fcType="scaledRetention",
    	sampleAnnoCol="test_ctrl",
    	sampleAnnotation=c("ctrl", "test"),
    	silent=TRUE, group=c(), pseudoFpkm=1, log2=TRUE)

    lfcEdgeRFpkm<- lfc(mdsChr22Obj, fcType="edgeR",
    	sampleAnnoCol="test_ctrl",
    	sampleAnnotation=c("ctrl", "test"),
    	silent=TRUE, group=c(), pseudoFpkm=1, log2=TRUE)

[Package IntEREst version 1.16.0 Index]