Find differential exon usage, etc.

edger_group_confects(fit, group_id, group_effect, fdr = 0.05, step = 0.01)

limma_group_confects(object, group_id, group_effect, fdr = 0.05,
  step = 0.01, trend = FALSE)

Arguments

fit

For edgeR, an edgeR DGEGLM object.

group_id

A factor of length nrow(fit), assigning items to groups (eg genes).

group_effect

A group effect object created by one of the A group_effect_... functions.

fdr

False Discovery Rate to maintain.

step

Step size when calculating confident effect sizes.

object

For limma, an expression matrix or EList object, or anything limma's lmFit will accept.

trend

For limma, should eBayes(trend=TRUE) be used?

Value

See nest_confects for details of how to interpret the result.

Details

If the order of the members of a group is important, ensure the order of rows is correct in the original matrix.

Groups with less than two members will be ignored.

To construct a group design matrix, the design from fit will be repeated in a block diagonal matrix.