#analysisMethods

Analysis Methods Module is a final module from SEPA (Simulation, Execution, Parse and Analysis, a multi pipe to test pathogen software detection), that analyze a cvs file provided by Parse Module (or your own cvs file in particular format), the analysis aviable are R², RRMSE (relative error) and ROC Curve

##Requirements

• Bash version 4 (comes with Linux and MacOSX)
• Internet connection if your realdata file (maybe metasim_conf_file.mprf or same format [abundance 'gi or ti' ginumber]) contain Genomes ID (gi)

##Usage analysisMethods provide three methods for the csv file:

• R² (determination coefficient)
• RRMSE (relative root mean square error)
• ROC Curve (receiver operating characteristic)

you need to specify what analysis you want in the configuration file like this:

# parseMethods configuration file (config.conf)#
# add comments using the pound character

ANALYSISTYPE=ROC_CURVE,R2,RMS_RE
TOTALGENOMES=426

#ANALYSISTYPE is a flag that specify the analysis that you want to do.
#TOTALGENOMES is a flag that you need to specify if ROC CURVE analysis is specified. its mean the universe of genomes (data base) that you used in mapping step (all genomes)

in example, three methods are required, can be only RMS_RE too or whatever.

Next, make sure you have a csv file provided by Parse Module that have the following format:

Superkingdom,Phylum,Class,Order,Family,Genus,Specie,Name,ti,filename1,filename2,filenameN
Bacteria,Firmicutes,Bacilli,Bacillales,Staphylococcaceae,Staphylococcus,Staphylococcus epidermidis,Staphylococcus epidermidis RP62A,"176279",20286,19568,19784,19562
Bacteria,Firmicutes,Bacilli,Bacillales,Bacillaceae,Bacillus,Bacillus anthracis,Bacillus anthracis str. CDC 684,"568206",86380,85306,85925,87788

Where the first eight column names are the complete lineage of the pathogen, ti is a NCBI taxonomy identifier, and filenameX is the number of reads that software mapped on corresponding ti and saved in file called filenameX.

Also you can provide your own csv file without lineage (or within) like this:

ti,filename1,filename2,filenameN
176279,20286,19568,19784,19562
568206",86380,85306,85925,87788
etc,etc,etc,etc,etc

Then you can execute the module typing the following command:

bash analysisMethods.bash --workpath [files directory] --cfile [config file] --simdata [simulation table csv format (',' separated)] --realdata [mconf from metasim] --local

####Options explanation:

• --workpath path where directory tree or your files are (included requirement files)
• --cfile is the configuration file
• --local is if you don't use the other modules of SEPA
• --simdata is the csv file that contain the simulated data
• --realdata a file that contain the real values of reads distribution (.mprf of metasim)

Example output

R² (R2.dat):

Analysis	ID1000-sam	ID150-sam	ID300-sam	ID75-sam
R2			0.5906		0.6408		0.6379		0.6317

RRMSE (rms.dat):

Analysis ID1000-sam	ID150-sam	ID300-sam	ID75-sam
RRMSE	0.766182	0.580528	0.583302	0.593402
AVGRE	0.662465	0.468544	0.469835	0.480457

ROC Curve (ROC.dat):

file		fpr		  tpr
ID1000-sam	0.0311751 0.714286
ID150-sam	0.0311751 0.8
ID300-sam	0.0311751 0.8
ID75-sam	0.0311751 0.8