segmentAverage: Average read-counts of segments

In raim/segmenTools: Tools for Functional Genome Exploration

Average read-counts of segments

Description

Average read-count time-series of a genomic interval (segment). Note that the diverse attempts to smooth or filter read-counts before taking the averages did not give good results, and we remained using avg="mean" and no other transformations.

Usage

segmentAverage(
  rds,
  avg = "mean",
  mean.ratio = FALSE,
  rm.extreme = FALSE,
  endcut = 0,
  k = 1,
  endrule = "median"
)

Arguments

rds	matrix of read-count time-series
avg	function to use as average statistics, mean or median
mean.ratio	calculate the mean ratio over time of each read-count time-series before taking the total average
rm.extreme	remove extreme value reads, i.e., where the temporal mean is <0.1 or >0.9 of all means
endcut	fraction of the ends the genomic interval to remove before taking the total average
k	parameter k for the running median function runmed; the running median will be calculated only if k>1
endrule	parameter endrule for the running median function runmed

raim/segmenTools documentation built on Sept. 25, 2024, 5:38 p.m.