Obtain DE gene/isoform list at a certain FDR
output from EBSeqHMMTest function
Target FDR; default is 0.05
Function GetDECalls() 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.
a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs;
Output: output a list of genes that are DE in at least one condition in an RNA-seq experiment with multiple ordered conditions
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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)
Loading required package: EBSeq Loading required package: blockmodeling Loading required package: gplots Attaching package: 'gplots' The following object is masked from 'package:stats': lowess Loading required package: testthat Attaching package: 'EBSeqHMM' The following object is masked from 'package:EBSeq': f0 Conditions are ordered as: t1 t2 t3 t4 t5 Estimating parameters when expected FC = 2 iteration time 0 iteration time 0 iteration time 0.1 iteration time 0 Estimated expected FC 2
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