diffSplice2 | R Documentation |
This is a small improvement to the diffSplice
function
written by Gordon Smyth and Charity Law.
diffSplice2(fit, geneid, exonid = NULL, robust = FALSE, verbose = TRUE)
fit |
an |
geneid |
gene identifiers (as in |
exonid |
exon identifiers (as in |
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 |
An MArrayLM-class
object containing both exon
level and gene level tests. Results are sorted by geneid and by exonid
within gene.
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)
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