getDPStats            package:AnnBuilder            R Documentation

_F_u_n_c_t_i_o_n_s _t_o _r_e_a_d _i_n _t_h_e _s_t_a_t_i_s_t_i_c_s _a_b_o_u_t _a _d_a_t_a _p_a_c_k_a_g_e

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

     These functions generate a list showing the name, data of
     creation, number of genes for each rda file, and the actual number
     of genes that get mapped for each rda file.

_U_s_a_g_e:

     getDPStats(baseF, pkgName, pkgPath, saveList = TRUE, isFile = TRUE)
     getDate(pkgName, pkgPath, fromDesc)
     getProbeNum(pkgName, pkgPath, noNA = FALSE)
     matchProbes(baseF, pkgName, pkgPath, toMatch, isFile = TRUE)
     getPBased()
     formatABQCList(x)
     countMapping(rdaName, noNA = FALSE)

_A_r_g_u_m_e_n_t_s:

   baseF: 'baseF' a character string for the name of a file that is
          going to be used as the base file to calculate the total
          number of probes and matched probes by a data package. Set to
          "" if there is no base file

 pkgName: 'pkgName' a character string for the name of the data package
          of concern

 pkgPath: 'pkgPath' a character string for name of the path to which
          the data package is stored.

    noNA: 'noNA' a boolean to indicate whether counts will exclude
          entries with NA as the value.

saveList: 'sageList' a boolean indicating whether the results will be
          returned as a list only (FALSE) or saved to a file as well
          (TRUE)

 toMatch: 'toMatch' a vector of character strings for the names of the
          rda files whose keys will be matched against the probe ids of
          a base file (baseF)

       x: 'x' a list object produced by function 'getDPStats'

fromDesc: 'fromDesc' a boolean that will get a date from a DESCRIPTION
          file if set TRUE or the current date if FALSE

  isFile: 'isFile' a boolean that will be TRUE if 'baseF' is the name
          of a file

 rdaName: 'rdaName' a character string for the name of an rda file
          whose man page will be generated

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

     Date of creation is the date when the package was created using
     AnnBuilder and in most cases is not the date when the source file
     AnnBuilder used to create the rda files was created. The date when
     the source data were built are listed in the man page for the
     package (?package name).

     The number of genes and number of genes mapped normally differ
     because not all genes in a given set can be mapped to annotation
     data. For probe based rda files (e. g. maps Affymetrix ids to
     annotation data), the number of mapped genes out of the total is
     given. For non-probe based rda files, only the total number of
     mapped items is given.

     The total number of probes of each rda file will be checked
     against the total of the base file and the names of the rda files
     whose total is off will be listed.

_V_a_l_u_e:

    list: A list with name and value pairs

_N_o_t_e:

     This function is part of the Bioconductor project at Dana-Farber
     Cancer Institute to provide Bioinformatics functionalities through
     R

_A_u_t_h_o_r(_s):

     Jianhua Zhang

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

     'ABPkgBuilder'

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

     # Run this code after changing the settings correctly
     # Change the varaibles before you run the code
     pkgName <- "hgu95a"
     pkgPath <- "where/your/data/package/is"
     # Call getABStats
     # getDPStats(pkgName, pkgPath)

