Description Usage Arguments Details Value Note Author(s) Examples
View source: R/GetConfidentCalls.R
Obtain confident gene calls for classifying genes into expression paths
1 | GetConfidentCalls(EBSeqHMMOut, FDR=.05, cutoff=0.5, OnlyDynamic=TRUE,Paths=NULL)
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EBSeqHMMOut |
output from EBSeqHMMTest function |
FDR |
Target FDR, default is 0.05. |
cutoff |
cutoff to use for defining a confident call. Genes with PP_path greater or equal to cutoff will be called as a confident call. Default is 0.5. |
OnlyDynamic |
if specifies as T, only dynamic paths will be shown |
Paths |
paths that are of interest. Default is NULL. If it is not specified, all possible paths will be considered. |
Function GetConfidentCalls() can be used to obtain a list of DE genes/isoforms with user specific cutoffs. To obtain a list of DE genes/isoforms with a target FDR alpha, the user may specify FDR=alpha. To further choose genes/isoforms with high posterior probability of being its most likely path, the user may specify the option cutoff (default is 0.5). Then genes or isoforms with PP(most likely path ) > = 0.5 will be selected
Overall: a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs; EachPath: a list object, each sublist contains confident calls (genes/isoforms) that have PP(path)>=cutoff for a particular expression path, shown are their names and PPs; NumEach: length of each sublist in EachPath. EachPathName: gene/isoform names in each of the sublists in EachPath
Output: output a list of genes that are classified to a expression path as a confident assignment.
Ning Leng
1 2 3 4 5 6 7 8 | data(GeneExampleData)
CondVector <- rep(paste("t",1:5,sep=""),each=3)
Conditions <- factor(CondVector, levels=c("t1","t2","t3","t4","t5"))
Sizes <- MedianNorm(GeneExampleData)
EBSeqHMMGeneOut <- EBSeqHMMTest(Data=GeneExampleData, sizeFactors=Sizes, Conditions=Conditions,
UpdateRd=2)
GeneDECalls <- GetDECalls(EBSeqHMMGeneOut, FDR=.05)
GeneConfCalls <- GetConfidentCalls(EBSeqHMMGeneOut, FDR=.05,cutoff=.5, OnlyDynamic=TRUE)
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