This is the command fitgcp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
fitgcp - fit mixtures of probability distributions to genome coverage profiles
SYNOPSIS
fitgcp [options] NAME
DESCRIPTION
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
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