NetAffxResource-class     package:AffyCompatible     R Documentation

_M_a_n_a_g_e _N_e_t_A_f_f_x _a_n_n_o_t_a_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class is for accessing and retrieving NetAffx annotation
     files for Affymetrix chips. It requires that the user has
     established an account with Affymetrix. Detailed usage is
     described in the `Annotations with NetAffx' vignette.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are created by calls of the form
     'NetAffxResource(user="user@research.org", password="terces")', as
     illustrated below and in the `Annotations with NetAffx vignette.

_S_l_o_t_s:


     '_u_s_e_r': Object of class '"character"' containing the full user
          name (typically an email address) obtained when the user
          registers with Affymetrix.

     '_p_a_s_s_w_o_r_d': Object of class '"character"' containing the password
          associated with the Affymetrix user name. The password is
          entered and stored in plain text, and should not be
          considered secure within Bioconductor.

     '_a_f_f_x_L_i_c_e_n_c_e': Object of class '"character"' containing the
          licence, obtained from Affymetrix, for retrieving NetAffx
          annotations. The licence is usually software specific (e.g.,
          for the AffyCompatible package of Bioconductor). Users will
          not usually change the defeault value.

     '_d_i_r_e_c_t_o_r_y': Object of class '"character"', containing the local
          directory path where the NetAffx data base and annotation
          files will reside.

     '_a_n_n_o_t_a_t_i_o_n_s_F_i_l_e': Object of class '"character"' containing the
          file name of the NetAffx data base. Users will not usually
          change the default value.

     '_a_f_f_x_U_r_l': Object of class '"character"' containing the URL used
          to download the NetAffx annotations file. Users will not
          usually change the default value.

_E_x_t_e_n_d_s:

     Class '"NetAffxCompatibility"', directly. Class
     '"AffyCompatible"', by class "NetAffxCompatibility", distance 2.

_M_e_t_h_o_d_s:


     [[ 'signature(x = "NetAffxResource", i = "numeric", j =
          "missing")'

     [[ 'signature(x = "NetAffxResource", i = "character", j =
          "missing")': Retrieve an object representing all NetAffx
          annotations available for an array. The argument 'i' may be a
          numeric index or character string corresponding to an array
          name returned by 'names(x)'.

     [[ 'signature(x = "NetAffxResource", i = "numeric", j =
          "numeric")'

     [[ 'signature(x = "NetAffxResource", i = "character", j =
          "numeric")'

     [[ 'signature(x = "NetAffxResource", i = "numeric", j =
          "character")'

     [[ 'signature(x = "NetAffxResource", i = "character", j =
          "character")': Retrieve an object representing a specific
          annotation for an array. The argument 'i' may be a numeric
          index or character string corresponding to an array name
          returned by 'names(x)'. The argument 'i' may be a numeric
          index or character string corresonding to an annotation
          returned by 'description(x[[i]])'.

     _a_f_f_x_L_i_c_e_n_c_e 'signature(x = "NetAffxResource")':  the character
          string representation of the licence used to access the
          NetAffx site.

     _a_f_f_x_U_r_l 'signature(x = "NetAffxResource")': the url used to access
          the NetAffx site.

     _a_n_n_o_t_a_t_i_o_n_s_F_i_l_e 'signature(x = "NetAffxResource")': the file name
          of NetAffx data base, as stored on the local disk of the
          user.

     _d_i_r_e_c_t_o_r_y 'signature(x = "NetAffxResource")': the directory in
          wich the NetAffx data base and annotation files are stored on
          the local disk of the user.

     _n_a_m_e_s 'signature(x = "NetAffxResource")': the names of the arrays
          for which annotations are available.

     _p_a_s_s_w_o_r_d 'signature(x = "NetAffxResource")': The password
          associated with the user name obtained when the user
          registered with Affymetrix. The password is entered and
          stored as plain text, and is not secure.

     _r_e_a_d_A_n_n_o_t_a_t_i_o_n 'signature(netAffxResource = "NetAffxResource",
          array = "numeric", annotation = "numeric", ...)'

     _r_e_a_d_A_n_n_o_t_a_t_i_o_n 'signature(netAffxResource = "NetAffxResource",
          array = "numeric", annotation = "character", ...)'

     _r_e_a_d_A_n_n_o_t_a_t_i_o_n 'signature(netAffxResource = "NetAffxResource",
          array = "character", annotation = "numeric", ...)'

     _r_e_a_d_A_n_n_o_t_a_t_i_o_n 'signature(netAffxResource = "NetAffxResource",
          array = "character", annotation = "character", ...)'

     _r_e_a_d_A_n_n_o_t_a_t_i_o_n 'signature(netAffxResource = "NetAffxResource",
          array = "missing", annotation = "AffxAnnotation", ...)': 
          Read a specific anntotation file as an R object. for the
          first four methods, 'array', if present, indexes or names the
          array while 'annotation' indexes or names the annotation. All
          methods also accept 'content = "logical"' to indicate whether
          the content of the file should be returned if possible
          ('content=TRUE', default) or only the path to the local file
          ('content=FALSE') and 'update = "logical"' indicating whether
          the file should be read from disk if available
          ('update=FALSE', default) or retrieved from the NetAffx web
          site ('update=TRUE'). 'readAnnotation' parses 'CSV, Tabular,
          PSI' to data frames, and reads 'FASTA' files to a list of
          description / sequence pairs (see 'Biostrings::readFASTA').

     _s_h_o_w 'signature(object = "NetAffxResource")': compactly show the
          'NetAffxResource' object.

     _u_s_e_r 'signature(x = "NetAffxResource")': The user name (typcially
          email address) obtained when the user registers with the
          Affymetrix web site.

_A_u_t_h_o_r(_s):

     Martin Morgan <mtmorgan@fhcrc.org>

_S_e_e _A_l_s_o:

     Vignette `Annotations with NetAffx'. Affymetrix user login site
     <URL: https://www.affymetrix.com/site/login/login.affx>.

     '.Rprofile' for ways to automatically set variables (such as
     'password', and 'directory') for each session.

_E_x_a_m_p_l_e_s:

     ## password must be obtained by the user
     rsrc <- NetAffxResource(user="mtmorgan@fhcrc.org", password=password)
     head(names(rsrc))
     affxDescription(rsrc[["Bovine"]])
     ## paradigm to display all elements of 'annotation'
     sapply(affxAnnotation(rsrc[["Bovine"]]), force)
     ## obtain and read a single annotation
     anno <- rsrc[["Porcine", "BLASTP annotations, CSV Format"]]
     df <- readAnnotation(rsrc, annotation=anno)

