PostFC: Calculate the posterior fold change for each transcript...

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

Calculate the posterior fold change for each transcript across conditions

Description

'PostFC' calculates the posterior fold change for each transcript across conditions.

Usage

PostFC(EBoutput, SmallNum = 0.01)

Arguments

EBoutput	The ourput from function EBTest.
SmallNum	A small number will be added for each transcript in each condition to avoid Inf and NA. Default is 0.01.

Value

Provide both FC and posterior FC across two conditions. FC is calculated as (MeanC1+SmallNum)/(MeanC2+SmallNum). And Posterior FC is calculated as:

# Post alpha P_a_C1 = alpha + r_C1 * n_C1

# Post beta P_b_C1 = beta + Mean_C1 * n_C1

# P_q_C1 = P_a_C1 / (P_a_C1 + P_b_C1)

# Post FC = ((1-P_q_C1)/P_q_c1) / ( (1-P_q_c2)/P_q_c2)

PostFC	The posterior FC across two conditions.
RealFC	The FC across two conditions (adjusted by the normalization factors).
Direction	The diretion of FC calculation.

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

EBTest, GetMultiFC

Examples

data(GeneMat)
GeneMat.small = GeneMat[c(500:550),]
Sizes = MedianNorm(GeneMat.small)
EBOut = EBTest(Data = GeneMat.small,
	Conditions = as.factor(rep(c("C1","C2"), each=5)),
	sizeFactors = Sizes, maxround = 5)
FC=PostFC(EBOut)

wiscstatman/EBSeq documentation built on June 3, 2023, 7:34 a.m.