diffSplice2 {diffUTR} | R Documentation

## 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)

[Package diffUTR version 1.0.0 Index]