segmentAverage: Average read-counts of segments

Description Usage Arguments

View source: R/segmenTools.R

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

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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 Nov. 9, 2018, 5:38 p.m.