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
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)