GetMultiFC: Calculate the Fold Changes for Multiple Conditions

In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

Description

'GetMultiFC' calculates the Fold Changes for each pair of conditions in a multiple condition study.

Usage

GetMultiFC(EBMultiOut, SmallNum = 0.01)

Arguments

EBMultiOut	The output of EBMultiTest function.
SmallNum	A small number will be added for each transcript in each condition to avoid Inf and NA. Default is 0.01.

Details

Provide the FC (adjusted by the normalization factors) for each pair of comparisons. A small number will be added for each transcript in each condition to avoid Inf and NA. Default is set to be 0.01.

Value

FCMat	The FC of each pair of comparison (adjusted by the normalization factors).
Log2FCMat	The log 2 FC of each pair of comparison (adjusted by the normalization factors).
PostFCMat	The posterior FC of each pair of comparison.
Log2PostFCMat	The log 2 posterior FC of each pair of comparison.
CondMean	The mean of each transcript within each condition (adjusted by the normalization factors).
ConditionOrder	The condition assignment for C1Mean, C2Mean, etc.

Author(s)

Ning Leng

References

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

See Also

EBMultiTest, PostFC

Examples

data(MultiGeneMat)
MultiGeneMat.small = MultiGeneMat[201:210,]

Conditions = c("C1","C1","C2","C2","C3","C3")

PosParti = GetPatterns(Conditions)
Parti = PosParti[-3,]

MultiSize = MedianNorm(MultiGeneMat.small)

MultiOut = EBMultiTest(MultiGeneMat.small, 
	NgVector=NULL, Conditions=Conditions, 
	AllParti=Parti, sizeFactors=MultiSize, 
	maxround=5)

MultiFC = GetMultiFC(MultiOut)

EBSeq documentation built on Nov. 8, 2020, 6:52 p.m.