filter.fragments: filter.fragments

In chicane: Capture Hi-C Analysis Engine

Description

Filter low and high-interacting restriction fragments based on the total number of trans counts

Usage

filter.fragments(
  interaction.data,
  bait.filters = c(0, 1),
  target.filters = c(0, 1),
  verbose = FALSE
)

Arguments

interaction.data	Data table containing interactions
bait.filters	Vector of length two, where the first element corresponds to the lower-end filter and the second to the upper-end filter. When global multiple testing correction is performed, altering the bait filtering settings may affect the number of significant results.
target.filters	Vector of length two, giving lower and higher filter, respectively. Changing this filtering setting may affect multiple testing correction by altering the number of tests performed.
verbose	Logical indicating whether to print progress reports.

Value

Data table containing fragments that passed all filters

Author(s)

Erle Holgersen <[e-mail]>

Examples

# filter out lowest 10% of baits
	filter.fragments(bre80, bait.filters = c(0.1, 1))

chicane documentation built on Nov. 7, 2021, 1:07 a.m.