GeneR                 package:GeneR                 R Documentation

_O_v_e_r_v_i_e_w _o_f _G_e_n_e_R _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     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.

_D_e_t_a_i_l_s:

     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 :

        *  In a C adapted class (buffers) that stores in addition some
           globals variables, like working strand, size of original
           sequence and so on.

           It is usefull when, for example, we have to work on a subset
           of a whole chromosome (i.e. a gene). In this case it will be
           worthwhile to load only the gene in R. Nevertheless, it will
           remain easy to associate positions on chromosome and
           positions on gene ...

           A complete description on this C class is given in page 
           'globals'.

        *  As a character string, the more logical way to store short
           sequences like "ATGTCGTG".  It concerns all functions like
           "strxxx" (strComp, strMultiExtract etc.).

     * 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).

_S_e_e _A_l_s_o:

     'globals', 'readSeq',  'readEmblLocation', 'getOrfs'

_E_x_a_m_p_l_e_s:

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

     ## Not run: 
     demo(hugeGeneR)
     ## End(Not run)

