GetDECalls: Obtain DE gene/isoform list at a certain FDR

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

Description

Obtain DE gene/isoform list at a certain FDR

Usage

GetDECalls(EBSeqHMMOut,FDR=.05)

Arguments

EBSeqHMMOut	output from EBSeqHMMTest function
FDR	Target FDR; default is 0.05

Details

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.

Value

a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs;

Note

Output: output a list of genes that are DE in at least one condition in an RNA-seq experiment with multiple ordered conditions

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)

Example output

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 

EBSeqHMM documentation built on Nov. 8, 2020, 5:22 p.m.