GeneR {GeneR}R Documentation

Overview of GeneR package

Description

GeneR packages allow direct use of nucleotide sequences within R software. Functions can be used to read and write sequences from main file formats (Embl, Genbank and Fasta) in order to perform a lot of manipulations and analyses. Main functions are implemented with C extensions.

Details

To summarize, we can split major functions into 4 categories.

I- Reading and writing sequences

GeneR has been designed for fast sequence retrieving even from very large sequence databanks, in Fasta, Embl or Genbank formats. It is also possible to enter sequences directly from a R command line.

There are two ways to store sequences :

II- Handling sequences

The usual copy-paste of parts of sequences or other manipulations can be performed by functions using vectors of strands and positions. Annotations from the features field within formatted sequence entries can be extracted and used directly in vectors. By this way, it is easy to extract sequence fragments of interest.

III- Analyzing sequences

Some tools are designed to count oligo-nucleotides, to look for exact word positions or to shuffle sequences (useful for statistical validations).

IV- Genetic tools

Finally, the package also contains functions related to genetic and structural aspects of the sequences : ORF localization, translation, or RNA secondary structure determination (with extension of GeneR: GeneRfold package).

See Also

globals, readSeq, readEmblLocation, getOrfs

Examples

## First of all you can try
demo(GeneR)

## Not run: 
demo(hugeGeneR)

## End(Not run)


[Package GeneR version 2.24.0 Index]