filterExtremePeakGenes: Filter out transcript by a median filter

In Roleren/ORFik: Open Reading Frames in Genomics

Filter out transcript by a median filter

Description

For removing very extreme peaks in coverage plots, use high quantiles, like 99. Used to make your plots look better, by removing extreme peaks.

Usage

filterExtremePeakGenes(
  tx,
  reads,
  upstream = NULL,
  downstream = NULL,
  multiplier = "0.99",
  min_cutoff = "0.999",
  pre_filter_minimum = 0,
  average = "median"
)

Arguments

tx	a GRangesList
reads	a GAlignments or GRanges
upstream	numeric or NULL, default NULL. if you want window of tx, instead of whole, specify how much upstream from start of tx, 10 is include 10 bases before start
downstream	numeric or NULL, default NULL. if you want window of tx, instead of whole, specify how much downstream from start of tx, 10 is go 10 bases into tx from start.
multiplier	a character or numeric, default "0.99", either a quantile if input is string[0-1], like "0.99", or numeric value if input is numeric. How much bigger than median / mean counts per gene, must a value be to be defined as extreme ?
min_cutoff	a character or numeric, default "0.999", either a quantile if input is string[0-1], like "0.999", or numeric value if input is numeric. Lowest allowed value
pre_filter_minimum	numeric, default 0. If value is x, will remove all positions in all genes with coverage < x, before median filter is applied. Set to 1 to remove all 0 positions.
average	character, default "median". Alternative: "mean". How to scale the multiplier argument, from median or mean of gene coverage.

Value

GRangesList (filtered)

Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.