App-easyDifferentialGeneCoexpressionWrapper
view release on metacpan or search on metacpan
```diff
cpanm --uninstall App::easyDifferentialGeneCoexpressionWrapper
```
On Linux Ubuntu, you might need to run the two previous CPAN commands as a superuser (`sudo cpanm App::easyDifferentialGeneCoexpressionWrapper` and `sudo cpanm --uninstall App::easyDifferentialGeneCoexpressionWrapper`).
## Execution instructions
The command for running easyDifferentialGeneCoexpressionWrapper is:
```diff
easyDifferentialGeneCoexpressionWrapper -a "PROBESETS_OR_GENE_SYMBOLS" -f "INPUT_FILE" -d "GEO_DATASET_CODE" -v "FEATURE_NAME" -v1 "CONDITION_1" -v2 "CONDITION_2" -o "OUTPUT_FILE"
```
An example usage command for computing the differential coexpression of probesets in the (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30201" target="_blank" rel="noopener noreferrer">GSE30201 gene expression dataset</a>) is:
```diff
easyDifferentialGeneCoexpressionWrapper -a "PROBESETS" -f "dc_probeset_list03.csv" -d "GSE30201" -v "source_name_ch1" -v1 "Patient" -v2 "Normal" -o result.out
```
When using this command, the output files of easyDifferentialGeneCoexpressionWrapper will be found in the `~/easyDifferentialGeneCoexpressionWrapper_files/results/` directory, created in the user's home directory.
The mandatory command line options are described below:
-a <PROBESETS_OR_GENE_SYMBOLS>
A flag to indicate type of data (probesets or gene symbols) being read during execution
-f <INPUT_FILE>
The name of the CSV file listing the probesets or the gene symbols
-d <GEO_DATASET_CODE>
GEO dataset code of the microarray platform for which the probeset-gene symbol mapping should be done
-v <FEATURE_NAME>
Name of the feature of the dataset that contains the two conditions to investigate
-v1 <CONDITION_1>
Name of the first condition in the feature to discriminate (for example, "healthy")
-v2 <CONDITION_2>
Name of the second condition in the feature to discriminate (for example, "can-
cer")
-o <OUTPUT_FILE>
Name of the output file where the output data for the differential coexpression of probesets are written
<p>Help information can be read by typing the following command:</p>
```diff
easyDifferentialGeneCoexpressionWrapper -h
```
bin/easyDifferentialGeneCoexpressionWrapper view on Meta::CPAN
# #
# 1. cURL: If using an Ubuntu-based system, the program will assist the user in installing cURL, otherwise #
# manual installation is required. #
# #
# 2. R programming language: >= v4 is required to be installed. #
# #
# #
# Program Usage: #
# -------------- #
# #
# easyDifferentialGeneCoexpressionWrapper -h [-a PROBESETS_OR_GENE_SYMBOLS] [-f INPUT_FILE] [-d GEO_DATASET_CODE] [-v FEATURE_NAME] [-v1 CONDITION_1] [-v2 CONDITION_2] [-o OUTPUT_FILE] #
# #
##########################################################################################################################################################################################
#import standard Perl modules
use strict;
use warnings;
use Term::ANSIColor;
use Getopt::Long qw(GetOptions);
bin/easyDifferentialGeneCoexpressionWrapper view on Meta::CPAN
my $month = $mon + 1;
my $year = $yr + 1900;
return "$year-0$month-$mday\_h$time_hour$time_minutes";
}
############################ SUBROUTINE 4 #######################################################
#This subroutine checks all command line input switches and arguments (including optional ones).
#It warns user if mandatory command line input switches and arguments are missing.
sub input_parameters_check {
my $help_message1 = "Usage: easyDifferentialGeneCoexpressionWrapper -h [-a PROBESETS_OR_GENE_SYMBOLS] [-f INPUT_FILE] [-d GEO_DATASET_CODE] [-v FEATURE_NAME] [-v1 CONDITION_1] [-v2 CONDITION_2] [-o OUTPUT_DIRECTORY]";
my $help_message2 = "Mandatory arguments:
-a PROBESETS_OR_GENE_SYMBOLS
-f user-specified CSV file
-d GEO dataset code
-v feature name
-v1 condition 1
-v2 condition 2
-o output results file
-h show help message and exit\n";
bin/easyDifferentialGeneCoexpressionWrapper view on Meta::CPAN
=pod
=encoding utf8
=head1 NAME
easyDifferentialGeneCoexpressionWrapper is a wrapper program for the easyDifferentialGeneCoexpression.r R script (developed by Davide Chicco).
=head1 SYNOPSIS
Usage: easyDifferentialGeneCoexpressionWrapper -a "PROBESETS_OR_GENE_SYMBOLS" -f "INPUT_FILE" -d "GEO_DATASET_CODE" -v "FEATURE_NAME" -v1 "CONDITION_1" -v2 "CONDITION_2" -o "OUTPUT_FILE"
An example usage command for computing the differential coexpression of probesets in the GSE30201 gene expression dataset is:
$ easyDifferentialGeneCoexpressionWrapper -a "PROBESETS" -f "dc_probeset_list03.csv" -d "GSE30201" -v "source_name_ch1" -v1 "Patient" -v2 "Normal" -o result.out
When using this command, the output files of easyDifferentialGeneCoexpressionWrapper will be found in the `~/easyDifferentialGeneCoexpressionWrapper_files/results/` directory, created in the user's home directory.
=head1 DESCRIPTION
This is a wrapper program for easyDifferentialGeneCoexpression.r whose function is to detect pairings of genes/probesets with the highest, significant differential coexpression. For more information, see its man page on CRAN (L<user manual|https://cr...
bin/easyDifferentialGeneCoexpressionWrapper view on Meta::CPAN
$ cpanm App::easyDifferentialGeneCoexpressionWrapper
To uninstall:
$ cpanm --uninstall App::easyDifferentialGeneCoexpressionWrapper
=head1 EXECUTION INSTRUCTIONS
The command for running easyDifferentialGeneCoexpressionWrapper is:
$ easyDifferentialGeneCoexpressionWrapper -a "PROBESETS_OR_GENE_SYMBOLS" -f "INPUT_FILE" -d "GEO_DATASET_CODE" -v "FEATURE_NAME" -v1 "CONDITION_1" -v2 "CONDITION_2" -o "OUTPUT_FILE"
An example usage command for computing the differential coexpression of probesets in the GSE30201 gene expression dataset is:
$ easyDifferentialGeneCoexpressionWrapper -a "PROBESETS" -f "dc_probeset_list03.csv" -d "GSE30201" -v "source_name_ch1" -v1 "Patient" -v2 "Normal" -o result.out
When using this command, the output files of easyDifferentialGeneCoexpressionWrapper will be found in the `~/easyDifferentialGeneCoexpressionWrapper_files/results/` directory, created in the user's home directory.
The mandatory command line options are described below:
-a <PROBESETS_OR_GENE_SYMBOLS>
A flag to indicate type of data (probesets or gene symbols) being read during execution
-f <INPUT_FILE>
The name of the CSV file listing the probesets or the gene symbols
-d <GEO_DATASET_CODE>
GEO dataset code of the microarray platform for which the probeset-gene symbol mapping should be done
-v <FEATURE_NAME>
name of the feature of the dataset that contains the two conditions to investigate
-v1 <CONDITION_1>
name of the first condition in the feature to discriminate (for example, "healthy")
-v2 <CONDITION_2>
name of the second condition in the feature to discriminate (for example, "can-
cer")
-o <OUTPUT_FILE>
name of the output file where the output data for the differential coexpression of probesets are written
=head1 HELP
Help information can be read by typing the following command:
$ easyDifferentialGeneCoexpressionWrapper -h
This command will print the following instructions:
( run in 0.585 second using v1.01-cache-2.11-cpan-c6e0e5ac2a7 )