diffSpliceDGEWrapper | R Documentation |
Wrappers around commonly-used DEU methods
(diffSpliceDGE
, DEXSeq
and an
improved version of diffSplice
diffSpliceDGEWrapper( se, design, coef = NULL, QLF = TRUE, robust = TRUE, countFilter = TRUE, excludeTypes = NULL ) diffSpliceWrapper( se, design, coef = NULL, robust = TRUE, improved = TRUE, countFilter = TRUE, excludeTypes = NULL ) DEXSeqWrapper( se, design = ~sample + exon + condition:exon, reducedModel = ~sample + exon, excludeTypes = NULL, ... )
se |
A bin-wise SummarizedExperiment as produced by
|
design |
A formula (using columns of 'colData(se)') or (for 'diffSpliceWrapper' or 'diffSpliceDGEWrapper' only) a model.matrix. |
coef |
The coefficient to be tested (ignored for 'DEXSeqWrapper'). |
QLF |
Logical; whether to use edgeR's quasi-likelihood negative binomial (applicable only to 'diffSpliceDGEWrapper'). |
robust |
Logical; whether to use robust fitting for the dispersion trend (ignored for 'DEXSeqWrapper'). |
countFilter |
Logical; whether to filter out low-count bins (ignored for 'DEXSeqWrapper'). |
excludeTypes |
A vector of bin types to ignore for testing. To test
for any kind of differential usage, leave empty. To test for differential
UTR usage, use 'excludeTypes=c("CDS","non-coding")' (or see
|
improved |
Logical; whether to use |
reducedModel |
A reduced formula (applicable only to 'DEXSeqWrapper'). |
... |
Further arguments (passed to 'testForDEU' and 'estimateExonFoldChanges') of 'DEXSeq'. Can for instance be used to enable multithreading, by passing 'BPPARAM=BiocParallel::MulticoreParam(ncores)'. |
The 'se' object with additional rowData columns contain bin (i.e. exon) -level statistics, and a metadata slot containing gene level p-values.
library(SummarizedExperiment) data(example_bin_se) se <- diffSpliceWrapper(example_bin_se, ~condition) head(rowData(se))
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