An Efficient Pseudomedian Filter for Tiling Microrrays

Thomas E. Royce, Nicholas J. Carriero, Mark B. Gerstein

Source Code



Linux / Macintosh
Microsoft Windows


./running_pseudomedian -i <input file> -b <span> -o <output file> -a <algorithm>

<input file> := tab delimited text file - first column is chromosome (eg chr1), second column is genomic position, third, fourth, etc are data columns. The file must be sorted by chromosome and position.
<span> := number of nucleotides on either side of probe being smoothed
<output file> := smoothed result
<algorithm> := either def, monahan, or msl
def := naive implementation
monahan := Monahan modification
msl := Monahan modification + skip list

Example Datasets

synthetic data

ENCODE ChIP-chip data