createSession: Create patternCNV session object

In hshdndx/new-to-CNV: patternCNV: a versatile tool for detecting copy number changes from exome-seq data

Description

This function loads a given configuration file, and initialize a patternCNV session object with input sample information, exon information and output directories.

Usage

createSession(config.file)

Arguments

config.file

the name of the configuration file which the patternCNV session information is to be read from. If it does not contain an absolute path, the file name is relative to the current working directory. The name could also be a URL.

Details

Configuratio file defines paths used by patternCNV functions. These include paths to where the results will be written and paths to the sample info config file along with the Exon Key.

Example configuration file:

plot_output_DIR = '/path/to/plot_output/'

txt_output_DIR = '/path/to/txt_output/'

exon_key_file = '/path/to/PatternCNV.Exon.Key.txt'

sample_info_file ='/path/to/sample_info.txt'

Value

An object of PatCNVSession-class

Author(s)

Chen Wang

See Also

Scan exome coverage of multiple samples scanMultiCovg; compute CNV log2-ratio values of multiple samples computeMultiCNV

Examples

##  load a simulation example
config.filename <- 'sim1.ini'
makeSimulation(config.filename)
sim.session <- createSession(config.filename)
  
##-- print basic session information
summary(sim.session)

hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.