scoreSegments {tilingArray}R Documentation

Score segments

Description

Score the segments found by a previous call to findSegments by comparing to genome annotation

Usage

scoreSegments(s, gff, 
  nrBasePerSeg = 1500, 
  probeLength  = 25,
  params = c(overlapFraction = 0.5, oppositeWindow = 100, flankProbes=10),
  verbose = TRUE)

Arguments

s environment. See details.
gff GFF dataframe.
nrBasePerSeg Numeric of length 1. This parameter determines the number of segments.
probeLength Numeric of length 1.
params vector of additional parameters, see details.
verbose Logical.

Details

This function scores segments. It is typically called after a segmentation. For an example segmentation script, see the script segment.R in the scripts directory of this package. For an example scoring script, which loads the data and then calls this function, see the script scoreSegments.R.

Value

A dataframe with columns as described in the details section.

Author(s)

W. Huber <huber@ebi.ac.uk>

Examples






[Package tilingArray version 1.2.0 Index]