parseBPMAP            package:AffyTiling            R Documentation

_R_e_t_u_r_n_s _i_n_f_o_r_m_a_t_i_o_n _f_r_o_m _a _B_P_M_A_P _f_i_l_e _f_o_r _s_e_l_e_c_t _p_r_o_b_e_s _i_n _a_n _A_f_f_y_m_e_t_r_i_x _t_i_l_i_n_g _a_r_r_a_y.

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

     parseBPMAP takes as input the path to an Affymetrix BPMAP file,
     and data on any genomic intervals of particular interest to the
     analysis.  

     Returns a matrix, where rows represent each probe on the tiling
     array and columns representing the following information:
     "UniqueID"     - A unique ID for each probeset of the form:
     "Chromosome-Start" (if makeUniqueID == TRUE) "CHR"          -
     Chromosome on which the probe is located "Start"        - Genomic
     position in the BPMAP file "PMX"          - X index of the spot on
     the tiling array "PMY"          - Y index of the spot on the
     tiling array "SEQ"          - Sequence of the probe (if
     readProbeSeq == TRUE) "iID"          - The ID of the interval in
     which this probe is located (if an interval was passed)

     Note that passing a region of interest returns only probes in that
     genomic region.  If no region is specified, information is
     returned for all probes on the tiling array.

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

     parseBPMAP(filename, iID=NULL, iCHR=NULL, iSTART=NULL, iEND=NULL, recordIntervalIDs = FALSE, makeUniqueID = TRUE, readOnlyNCBI = TRUE, seqIndices = NULL, readProbeSeq = TRUE, verbose = 0)

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

filename: The path to the BPMAP file which describes the arrays
          specified in the cel files. 

     iID: Vector of IDs for each interval specified. 

    iCHR: Vector of chromosomes for each interval. 

  iSTART: Integer vector of the interval start. 

    iEND: Integer vector of the interval end. 

recordIntervalIDs: If TRUE, returns a column of the interval ID
          corresponding to each probe.  Requires use of interval data. 

makeUniqueID: If TRUE (default), returns a column of unique identifiers
          for each probe, of the form: "chr"-"start" 

readOnlyNCBI: If TRUE (default), returns ONLY probes that target NCBI
          sequences, TIGR and Affymetrix controls are ignored. 

seqIndices: If specified, reads only given portions of the BPMAP file
          (Expert ONLY). 

readProbeSeq: If TRUE, returns the first 25 bp of the probe sequence. 

 verbose: if >= 1, returns varying amounts of output in the R window. 

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

     Charles Danko

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

     ## Note that executing the following example requires a .bpmap file in the working directory.
     ## If one does not exist, the program will not execute.

     ## Identify a .bpmap file in the current working directory.
     BPMAP <- dir(pattern=".bpmap");

     ## If one or more .bpmap file are present in the current working directory
     ## returns a list representation of information in the first .bpmap file.
     if( NROW(BPMAP) > 0 ) {
       parseBPMAP(BPMAP[0]);
     }

