ilr_counts: Obtain an isometric log ratio transformed matrix from REPAC...

In eddieimada/REPAC: Differential Alternative Polyadenylation Analysis From Compositions

Obtain an isometric log ratio transformed matrix from REPAC results

Description

ilr_counts generates an sometric log ratio transformed matrix based on the References and Sites from a REPAC result.

Usage

ilr_counts(se, results)

Arguments

se	The (Ranged)SummarizedExperiment object used on the analysis.
results	A data.frame or tibble with results from REPAC

Value

An isometric log ratio transformed matrix.

Author(s)

Eddie Imada

Examples

## fit model and test for DPU
groups <- rep(c("A", "B"), each=5)
dMat <- model.matrix(~ 0+groups)
colnames(dMat) <-  gsub("groups", "",colnames(dMat))
cMat <- makeContrasts(
    levels=colnames(dMat),
    BvsA= B - A
)
results <- fit_repac(se, dMat, cMat)
results <- resolve_comparisons(results)
mat <- ilr_counts(se, results$BvsA)

eddieimada/REPAC documentation built on Aug. 20, 2023, 7:22 a.m.