addSignatures: Add molecular signatures to MultiAssayExperiment

In bkaczkowski/xcore: xcore expression regulators inference

Add molecular signatures to MultiAssayExperiment

Description

addSignatures extends mae by adding to it new experiments. Rows consistency is ensured by taking an intersection of rows after new experiments are added.

Usage

addSignatures(mae, ..., intersect_rows = TRUE)

Arguments

mae	MultiAssayExperiment object.
...	named experiments to be added to mae.
intersect_rows	logical flag indicating if only common rows across experiments should be included. Only set to FALSE if you know what you are doing.

Value

MultiAssayExperiment object with new experiments added.

Examples

data("rinderpest_mini", "remap_mini")
base_lvl <- "00hr"
design <- matrix(
  data = c(1, 0, 0,
           1, 0, 0,
           1, 0, 0,
           0, 1, 0,
           0, 1, 0,
           0, 1, 0,
           0, 0, 1,
           0, 0, 1,
           0, 0, 1),
  ncol = 3,
  nrow = 9,
  byrow = TRUE,
  dimnames = list(colnames(rinderpest_mini), c("00hr", "12hr", "24hr")))
mae <- prepareCountsForRegression(
  counts = rinderpest_mini,
  design = design,
  base_lvl = base_lvl)
mae <- addSignatures(mae, remap = remap_mini)

bkaczkowski/xcore documentation built on Jan. 26, 2024, 6:24 p.m.