filterSignatures: Filter signatures by coverage

In bkaczkowski/xcore: xcore expression regulators inference

Filter signatures by coverage

Description

Filter signatures overlapping low or high number of promoters. Useful to get rid of signatures that have very low variance.

Usage

filterSignatures(
  mae,
  min = 0.05,
  max = 0.95,
  ref_experiment = "Y",
  omit_experiments = c("Y", "U")
)

Arguments

mae	MultiAssayExperiment object.
min	length one numeric between 0 and 1 defining minimum promoter coverage for the signature to pass filtering.
max	length one numeric between 0 and 1 defining maximum promoter coverage for the signature to pass filtering.
ref_experiment	string giving name of experiment to use for inferring total number of promoters.
omit_experiments	character giving names of experiments to exclude from filtering.

Value

MultiAssayExperiment object with selected experiments filtered.

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)
mae <- filterSignatures(mae)

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