diffSplice2: diffSplice2

In ETHZ-INS/diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

diffSplice2

Description

This is a small improvement to the diffSplice function written by Gordon Smyth and Charity Law.

Usage

diffSplice2(fit, geneid, exonid = NULL, robust = FALSE, verbose = TRUE)

Arguments

fit	an MArrayLM-class fitted model object produced by lmFit or 'contrasts.fit', with rows corresponding to exons.
geneid	gene identifiers (as in diffSplice)
exonid	exon identifiers (as in diffSplice)
robust	logical, should the estimation of the empirical Bayes prior parameters be robustified against outlier sample variances?
verbose	logical, if TRUE will output some diagnostic information

Value

An MArrayLM-class object containing both exon level and gene level tests. Results are sorted by geneid and by exonid within gene.

Examples

library(SummarizedExperiment)
library(edgeR)
data(example_bin_se)
se <- example_bin_se
design <- model.matrix(~condition, data=as.data.frame(colData(se)))
dds <- calcNormFactors(DGEList(assays(se)$counts))
dds <- voom(dds, design)
dds <- lmFit(dds, design)
res <- diffSplice2(dds, geneid=rowData(se)$gene, exonid=row.names(se))
topSplice(res)

ETHZ-INS/diffUTR documentation built on Nov. 3, 2024, 6:26 p.m.