fitgcp1

Fit mixtures of probability distributions to genome coverage profiles

Usage

fitgcp [options] NAME

Overview

Fits mixtures of probability distributions to genome coverage profiles using an EM-like iterative algorithm.

The script uses a SAM file as input and parses the mapping information and creates a Genome Coverage Profile (GCP). The GCP is written to a file, such that this step can be skipped the next time. The user provides a mixture model that is fitted to the GCP. Furthermore, the user may specify initial parameters for each model.

As output, the script generates a text file containing the final set of fit parameters and additional information about the fitting process. A log file contains the the current set of parameters in each step of the iteration. If requested, a plot of the GCP and the fitted distributions can be created.

Options

NAME: Name of SAM file to analyze.

-h, --help: show this help message and exit

-d DIST, --distributions=DIST: Distributions to fit. z->zero; n: nbinom (MOM); N: nbinom (MLE); p:binom; t: tail. Default: zn

-i STEPS, --iterations=STEPS: Maximum number of iterations. Default: 50

-t THR, --threshold=THR: Set the convergence threshold for the iteration. Stop if the change between two iterations is less than THR. Default: 0.01

-c CUTOFF, --cutoff=CUTOFF: Specifies a coverage cutoff quantile such that only coverage values below this quantile are considered. Default: 0.95

-p, --plot: Create a plot of the fitted mixture model. Default: False

-m MEAN, --means=MEAN: Specifies the initial values for the mean of each Poisson or Negative Binomial distribution. Usage: -m 12.4 -m 16.1 will specify the means for the first two non-zero/tail distributions. The default is calculated from the data.

-a ALPHA, --alpha=ALPHA: Specifies the initial values for the proportion alpha of each distribution. Usage: For three distributions -a 0.3 -a 0.3 specifies the proportions 0.3, 0.3 and 0.4. The default is equal proportions for all distributions.

-l, --log: Enable logging. Default: False

--view: Only view the GCP. Do not fit any distribution. Respects cutoff (-c). Default: False