Filter signatures by coverage

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)