geneLevelStats | R Documentation |
Aggregates bin-level statistics to the gene-level
geneLevelStats( se, coef = NULL, excludeTypes = NULL, includeTypes = NULL, returnSE = TRUE, minDensityRatio = 0.1, minWidth = 20, excludeGeneAmbiguous = TRUE )
se |
A 'RangedSummarizedExperiment' containing the results of one of the DEU wrappers. |
coef |
The coefficients tested (if the model included more than one term). |
excludeTypes |
Vector of bin types to exclude. |
includeTypes |
Vector of bin types to include (overrides 'excludeTypes') |
returnSE |
Logical; whether to return the updated 'se' object (default), or the gene-level table. |
minDensityRatio |
Minimum ratio of read density (with respect to the gene's average) for a bin to be included. |
minWidth |
Minimum bin width to include |
excludeGeneAmbiguous |
Logical; whether to exclude bins which are ambiguous (i.e. can be from different genes) |
If 'returnSE=TRUE' (default), returns the 'se' object with an updated 'metadata(se)$geneLevel' slot, otherwise returns the gene-level data.frame.
library(SummarizedExperiment) data(example_bin_se) se <- diffSpliceWrapper(example_bin_se, ~condition) se <- geneLevelStats(se, includeTypes="3UTR") head(metadata(se)$geneLevel)
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