GetConfidentCalls: Obtain confident gene calls for classifying genes into...

In lengning/EBSeqHMM: Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments

Description

Obtain confident gene calls for classifying genes into expression paths

Usage

GetConfidentCalls(EBSeqHMMOut, FDR=.05, cutoff=0.5, OnlyDynamic=TRUE,Paths=NULL)

Arguments

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.

Details

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

Value

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

Note

Output: output a list of genes that are classified to a expression path as a confident assignment.

Author(s)

Ning Leng

Examples

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)

lengning/EBSeqHMM documentation built on May 21, 2019, 4:02 a.m.