plotReadsRepartitionAnnotations: Graphical information about reads and annotations repartition
In Pasha: Preprocessing of Aligned Sequences from HTS Analyses

Description Usage Arguments Details Value Author(s)

This function plots from an internal alignedData object the number of annotations per chromosome, the number of annotations by file, the number of reads per chromosome, the length of chromosomes, the percentage of coverage of each annotation according to the size of the reference genome and the number of reads of the reference experiment that aligned to a given annotation.

 
plotReadsRepartitionAnnotations(alignedData,  
                                gff_names_vec, 
                                expName,
                                pdfFileName, 
                                genomeReferenceFile)

`alignedData`	An internal R object containing information about the aligned reads
`gff_names_vec`	A vector containing all file pathes to annotations in gff format
`expName`	A character string giving the name of the reference experiment from which information about reads alignment were retrieved
`pdfFileName`	The file path to the pdf output
`genomeReferenceFile`	File path to the reference genome in .ref format (see details)

The pdf output is divided into three pages:

- The first page contains 4 barplots giving respectively the number of each annotation by chromosomes (seqnames) (the correspondence between colors and annotations is given at the bottom), the number of annotations contained in each file of gff_names_vec argument, the number of reads that aligned to each chromosome and the length of each chromosome.

- The second page contains two pie charts: The first one gives the percentage of coverage of the reference genome by each annotation, correspondence of colors is given at the right of the pie chart. The second pie chart gives the percentage of reads that aligned to a particular annotation, correspondence of colors is also given at the right of the pie chart.

- The third page is another representation of the pie chart enabling to compare directly the difference of occupancy of each annotation with the number of reads aligned to it.

The 'genomeReferenceFile' is the path to a file containing information about the genome that has been used to align the reads. It is a 3 lines text files.

The same files are used for multiread (see vignette).

Some files are provided in the package for some of the most commonly used genomes. For a list of them type:

dir(pattern="*.ref", path=system.file("resources", package="Pasha"))

First line describes the number of chromosomes in the genomes. Second line contains the size (in bp) of all chromosomes (space separated). Last lines containes the names of the chromosomes (space separated).

Example : 3 43255 10345 2456 chrI chrII chrIII

A pdf file with different graphics representing information described in the details section.

Nicolas Descostes

Pasha documentation built on Jan. 15, 2017, 6:21 p.m.