readBGX              package:beadarray              R Documentation

_R_e_a_d _I_l_l_u_m_i_n_a _b_g_x _f_i_l_e _i_n_t_o _R

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

     Reads in unzipped Illumina .bgx file, which provides further
     information on each bead type, including the controls.

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

     readBGX(filename, path=".", sep="\t", quote="", header=TRUE,
                probeStart="\[Probes\]", controlStart="\[Controls\]", ...)

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

filename: character vector specifying name of unzipped bgx file

    path: character string specifying the location of the bgx file

     sep: separator character (default is tab, '"\t"')

   quote: character string specifying the quoting characters (disabled
          by default with 'quote=""').  See 'scan' for further
          information.

  header: logical, TRUE if the bgx file has a header, FALSE otherwise

probeStart: character string, below which the information for the beads
          of interest appear. Default value is "\[Probes\]"

controlStart: character string, below which the information for the
          control beads appear. Default value is "\[Controls\]" 

     ...: further arguments to 'read.table'

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

     The .bgx file is a zip file which contains information about each
     probe on an expression BeadArray.

     To read in the file, you first need to unzip it. To do this,
     replace the .bgx extension with .zip (for example rename
     'HumanRef-8_V2_0_R0_11223162_A.bgx' as
     'HumanRef-8_V2_0_R0_11223162_A.zip') and then unzip this file
     (which should leave one file 'HumanRef-8_V2_0_R0_11223162_A' for
     our example). The unzipped file is tab delimited file and should
     be readable using 'readBGX'. At present this should work for Human
     and Rat expression arrays.  For Mouse arrays, the .bgx has a more
     complicated structure.

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

     data.frame containing information about each bead type (probe
     sequence, ID, control status, etc)

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

     Matt Ritchie

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

     #human8bgx = readBGX("HumanRef-8_V2_0_R0_11223162_A", fill=TRUE)
     #colnames(human8bgx)
     #summary(human8bgx$Status)
     #human6bgx = readBGX("HumanWG-6_V2_0_R0_11223189_A", fill=TRUE)
     #ratbgx = readBGX("RatRef-12_V1_0_R0_11222119_A", fill=TRUE)

