quantsmooth (version 1.38.0)

getChangedRegions: getChangedRegions

Description

retrieve regions of interest in a vector of intensities using quantile smoothing

Usage

getChangedRegions(intensities, positions, normalized.to=1, interval, threshold, minlength=2, ...)

Arguments

intensities

numeric vector

positions

numeric vector of the same length as intensities. If this argument is not given the results contain the indexes of the intensities vector, else the values in positions are used. Both vectors are sorted in the order of positions.

normalized.to

numeric, reference value. Changes are compared to this value

interval

numeric [0,1], bandwidth around reference. If the smoothed line at the higher quantile drops below the normalized.to value, a deleted region is recognized, and vice versa.

threshold

numeric, if the median smoothed value drops below normalized.to - threshold, or above normalized.to + threshold a changed region is called

minlength

integer, not used currently

...

extra arguments for quantsmooth function

Value

A data.frame with 3 colums is returned. Each row contains a region with columns up, start and end. start and end indicate positions in the vector of the first and last position that were up- or downregulated

Details

This function uses quantsmooth to detect regions in the genome that are abnormal. If interval is set then a smoothed line is calculated for tau = 0.5 - interval/2, and a region is determined as upregulated if this line is above the reference. Down regulation is determined when the smoothed line for tau = 0.5 + interval/2 is below the reference value. If threshold is set then a smoothed line is calculated for tau = 0.5 and up- or down regulation are determined when this line is outside the range [normalized.t - threshold:normalized.to + threshold]

Examples

  data(chr14)
  getChangedRegions(ill.cn[,1],ill.pos,normalized.to=2,interval=0.5)