deswish: deswish: DESeq2-apeglm With Inferential Samples Helps

In mikelove/fishpond: Fishpond: downstream methods and tools for expression data

deswish: DESeq2-apeglm With Inferential Samples Helps

Description

The DESeq2-apeglm With Inferential Samples implementation supposes a hierarchical distribution of log2 fold changes. The final posterior standard deviation is calculated by adding the posterior variance from modeling biological replicates computed by apeglm, and the observed variance on the posterior mode over inferential replicates. This function requires the DESeq2 and apeglm packages to be installed and will print an error if they are not found.

Usage

deswish(y, x, coef)

Arguments

y	a SummarizedExperiment containing the inferential replicate matrices, as output by tximeta, and then with labelKeep applied. One does not need to run scaleInfReps as scaling is done internally via DESeq2.
x	the design matrix
coef	the coefficient to test (see lfcShrink)

Value

a SummarizedExperiment with metadata columns added: the log2 fold change and posterior SD using inferential replicates, and the original log2 fold change (apeglm) and its posterior SD

References

The DESeq and lfcShrink function in the DESeq2 package:

Zhu, Ibrahim, Love "Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences" Bioinformatics (2018).

Love, Huber, Anders "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" Genome Biology (2014).

Examples

# a small example... 500 genes, 10 inf reps
y <- makeSimSwishData(m=500, numReps=10)
y <- labelKeep(y)
#y <- deswish(y, ~condition, "condition_2_vs_1")

mikelove/fishpond documentation built on Aug. 29, 2023, 2:45 p.m.