NAME

matchDistribution

SYNOPSIS

Given distinct "subject" (S) and a "target" (T) distributions, this script attempts to mimic T's density (i.e., its shape) by randomly sampling from bins in S's population.

Usage: matchDistribution.pl <OPTIONS> <arg1> <arg2> <arg3>

ARGUMENTS/INPUT

• arg1: Path to file containing T's values (1 column, 1 value per line).
• arg2: Number of bins to split the distributions into.
• arg3: Path to tab-separated file containing S's identifiers and values (column 1: unique identifier; column 2: corresponding value).

OPTIONS

• transform (string) = bin transform-transformed values in both distributions. Output values will be the original, non-transformed ones, though.

  Possible values: 'log10' only.

  Note: binning into log10-transformed is highly recommended e.g. for matching FPKM/RPKM distributions.

• verbose = make STDERR more verbose

OUTPUT

To STDOUT.

The script will output a pseudo-random subset of the subject file (i.e., arg3), such that its distribution matches T's density as closely as possible.

DESCRIPTION

Given distinct "subject" (S) and a "target" (T) distributions, this script attempts to mimic T's density (i.e., its shape) by pseudo-randomly sampling from S's population.

Warning: The script attempts to match T's density only, not its population size.

IMPORTANT NOTES

• "Pseudo-randomness"

  Items from S's population are randomly selected within bins, not within the entire population, hence the "pseudo" prefix

• Number of bins to choose

  Usually the more, the better.

• Log-transform

  Binning into log10-transformed is highly recommended e.g. for matching FPKM/RPKM distributions (see transform option).

• Re-iteration

  It might be necessary to call the script several times sequentially (i.e. input -> output1; output1 -> output2; output2 -> output3, etc., where "->" denotes a matchDistribution call) until reaching an optimum. This is what the accompanying matchDistributionLoop.sh script does (see below).

RE-ITERATIONS

Use matchDistributionLoop.sh and matchDistributionKStest.r. Both scripts need to be in your $PATH.

Usage: matchDistributionLoop.sh <passes> <doKolmogorov-Smirnov> <target> <subject> <bins> <breakIfKSTest>

Where:

• passes (int): Maximum number of passes to perform
• doKolmogorov-Smirnov (0|1 boolean): Toggle do KS test on resulting distributions after each pass, and print p-value. This will call matchDistributionKStest.r (courtesy of Andres Lanzos, CRG).
• target (string): Path to file containing T's values.
• subject (string): Path to tab-separated file containing S's identifiers and values.
• bins (int): Number of bins to split the distributions into.
• breakIfKSTest (0|1 boolean): break loop if KS test gives p>0.05 (i.e., before reaching the maximum number of passes).

DEPENDENCIES

CPAN: List::Util 'shuffle'

AUTHOR

Julien Lagarde, CRG, Barcelona, contact [email protected]