CNOGpro: Set up a new CNOGpro experiment
In CNOGpro: Copy Numbers of Genes in prokaryotes

Description Usage Arguments Details Value Author(s) References See Also Examples

This function initializes the CNOGpro experiment.

1 2	CNOGpro(hitsfile, gbkfile, windowlength = 100, name = "Default organism")

`hitsfile`	Path to a text file containing two columns: The first column is a chromosome identifier, and the second column is the leftmost coordinate (in the reference organism) of a mapped read. Each row represents one single read.
`gbkfile`	The GenBank Flat Format file of the organism used as a reference in the resequencing study. Must contain DNA sequence, not just annotations. Multi-chromosomal files are not currently supported, and should be parsed separately.
`windowlength`	Integer length of the sliding window which will be used when counting read density.
`name`	(Optional) A name of the organism or copy number experiment.

The function accepts a minimum input of the GenBank file, but will not be able to do any copy number analysis in this mode. As such, the primary use of this modes when the user just wants to print a table of genetic elements.

The hitsfile can be constructed from a SAMtools binary alignment/ map (.bam) file by entering the following at the shell command line:
samtools view infile.bam | perl -lane 'print \"$F[2]\t$F[3]\"' > out.hits

An object of class CNOGpro, which can be used in further CNV analysis. Essentially a list containing the following elements:

`Name`	The name of the organism or project, as set by this method.
`windowlength`	The length of the sliding window when counting reads
`accession`	The accession number of the chromosome, from the provided GenBank file
`genes`	A table of genetic elements in the chromosome, including intergenic regions. The table will also hold copy numbers as inferred from the `runHMM` and `runBootstrap` methods.
`chrlength`	The length of the chromosome
`GCperwindow`	The GC-percentage, calculated in sliding windows.
`is_GC_normalized`	logical indicating whether data has been normalized or not
`ReadsprWindow`	The (raw) read counts in sliding windows
`CorrReadsprWindow`	The read counts in sliding windows, corrected for GC bias. Acquired from the `normalizeGC` method.
`HMMtable`	The data frame of breakpoints and states inferred from the `runHMM` method.

Ola Brynildsrud (ola.brynildsrud@nmbu.no)

Manuscript not yet published.

normalizeGC, runBootstrap, runHMM, store

carsonella <- CNOGpro(hitsfile=system.file("extdata/carsonellahits.tab", package="CNOGpro"),
gbkfile=system.file("extdata/CP003467.gbk",package="CNOGpro"), windowlength=100,
name="Artificial Carsonella ruddii data")
plotCNOGpro(carsonella)
printCNOGpro(carsonella)