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Bio-SDRS-0.06
River stage zero No dependents
++
/ sdrs.pl

NAME

sdrs.pl - Command line script to use Bio::SDRS to run a Signmoidal Dose Response Search.

SYNOPSIS

    sdrs.pl -multiple=1.05 \
            -step=20 \
            -ldose=0.4 \
            -hdose=25000 \
            -trim=0 \
            -outdir=results \
            data/OVCAR4_HCS_avg.txt

OPTIONS

-multiple=<float>

Specifies the multiplicity factor for increasing the dose during the search. It must be greater than one.

-ldose=<float>

Specifies the minimum dose for the search. Must be greater than zero.

-hdose=<float>

Specifies the maximum dose for the search. Must be greater than the ldose above.

-step=<float>

This value specifies the maximum change in doses in the search. In the search process, this module starts at the ldose value. It tries multiplying the current dose by the multiple value, but it will only increase the dose by no more than the step value specified here. It must be positiv.e

-maxproc=<integer>

Specifies the maximum number of processes to be used in the search.

-trim=<float>

Trims the number of measurements used in the analysis by this factor. Must be a real number between zero and one, although zero makes no sense because no experiments would be used in the analysis.

-outdir=<directory>

Specifies the directory where the results are written. If this directory does not exist, it is created.

-[no]debug

Controls display of debugging information. Normally should be left off.

DESCRIPTION

This program provides a simple command line interface to the Bio::SDRS Perl module.

INPUT FILE

There is only one input file to this script which is meant to provide the data for one experiment. The file provides the doses of compound used in the experiment, and it provides the measurements for each dose for every compound used in the experiment. The file uses Tab Separated Value (TSV) format, with each value separated from each other using the Tab character (ASCII code 9).

The first line of the input file must contain the doses as floating point numbers, with a comment word as the first word. For example, the following line would describe a eight dose experiment.

Dose 0.42 1.27 3.81 11.43 34.29 102.88 308.64 925.92

The succeeding lines of the input file are the measured responses for each compound tested, with no limit to the number of compounds. The first word in each line is the name of the compound, and the remaining lines are the responses for each dose as specified in the dose line at the top of the file, and in the same order. Here is an example response line consistent with the dose example above:

Aspirin 2.1 1.695 1.675 1.735 1.56 1.77 2.34 2.595

OUTPUT FILES

The output files are written to the directory specified by the outdir option above. The names are composed in part from the options:

sdrs.multiple.step.out

The values of the sigmoidal function along with F-score for every tested value for every compound. Each line is a tab separated value containing the compound, dose, F-score for the fit, A, B, and D value.

sdrs.multiple.step.EC50.out

Provides all the EC50 data for each compound in the input file as a tab separated record. The columns are as follows:

 1  Compound
 2  MAX         Maximum F score
 3  MIN         Minimum F score
 4  LOW         Low value for the dose.
 5  HIGH        High value for the dose.
 6  EC50        EC50 for the dose search.
 7  PVALUE      F score P value
 8  EC50RANGE   Range of dose values where F score cutoff is satisfied.
 9  PEAK        Number of peaks in the F score.
10  A           A parameter in the sigmoid function.
11  B           B parameter in the sigmoid function.
12  D           D parameter in the sigmoid function.
13  FOLD        Positive Ratio of B/A or 99999.0 if a == 0.

sdrs.sorted_probes.out

For every calculated dose in the search, list the compounds in order of F score. Each line in this file is a TSV record where the first field is the calculated dose, and the remaining fields are the compound names.

sdrs.pval_FDR.out

For every calculated dose in the search, list the P Values for fit for the compounds in order of F score exactly in the same order as the sdrs.sorted_probes.out file. Each line in this file is a TSV record where the first field is the calculated dose, and the remaining fields are the compound names. This file is meant to be used in conjunction with the sdrs.sorted_probes.out files.

SEE ALSO

Bio::SDRS.

AUTHORS

 Ruiru Ji <ruiruji@gmail.com>
 Nathan O. Siemers <nathan.siemers@bms.com>
 Lei Ming <lei.ming@bms.com>
 Liang Schweizer <liang.schweizer@bms.com>
 Robert Bruccoleri <bruc@acm.org>