lfc {IntEREst} | R Documentation |
Log fold change estimation and normalized log fold change using edgeR
package.
lfc(x, fcType="edgeR", sampleAnnoCol=c(), sampleAnnotation=c(), silent=TRUE, group=c(), rejection.region="doubletail", pseudoCnt=1, log2=TRUE, ...)
x |
Object of type |
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 |
sampleAnnotation |
A vector of size 2 which cotains values from |
silent |
Whether run |
group |
Vector to manually define the sample groups (or annotations). It is ignored if
|
rejection.region |
The rejection.region parameter in |
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 |
Vector including fold change values.
Ali Oghabian
exactTestInterest
, u12DensityPlotIntron
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)