readBpmap             package:affxparser             R Documentation

_P_a_r_s_e_s _a _B_p_m_a_p _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Parses (parts of) a Bpmap (binary probe mapping) file from
     Affymetrix.

_U_s_a_g_e:

     readBpmap(filename, seqIndices = NULL, readProbeSeq = TRUE, readSeqInfo
     = TRUE, readPMXY = TRUE, readMMXY = TRUE, readStartPos = TRUE,
     readCenterPos = FALSE, readStrand = TRUE, readMatchScore = FALSE,
     readProbeLength = FALSE, verbose = 0)

     readBpmapHeader(filename)

     readBpmapSeqinfo(filename, seqIndices = NULL, verbose = 0)

_A_r_g_u_m_e_n_t_s:

filename: The filename as a character.

seqIndices: A vector of integers, detailing the indices of the
          sequences being read. If 'NULL', the entire file is being
          read.

readProbeSeq: 

readSeqInfo: Do we read the sequence information (a list containing
          information such as sequence name, number of hits etc.)

readPMXY: Do we read the (x,y) coordinates of the PM-probes.

readMMXY: Do we read the (x,y) coordinates of the MM-probes (only
          relevant if the file has MM information)

readStartPos: Do we read the start position of the probes.

readCenterPos: Do we return the start position of the probes.

readStrand: Do we return the strand of the hits.

readMatchScore: Do we return the matchscore.

readProbeLength: Doe we return the probelength.

 verbose: How verbose do we want to be.

_D_e_t_a_i_l_s:

     'readBpmap' reads a BPMAP file, which is a binary file containing
     information about a given probe's location in a sequence. Here
     sequence means some kind of reference sequence, typically a
     chromosome or a scaffold. 'readBpmapHeader' reads the header of
     the BPMAP file, and 'readBpmapSeqinfo' reads the sequence info of
     the sequences (so this function is merely a convinience function).

_V_a_l_u_e:

     For 'readBpmap': A list of lists, one list for every sequence
     read. The components of  the sequence lists, depends on the
     argument of the function call. For 'readBpmapheader' a list with
     two components 'version' and 'numSequences'. For
     'readBpmapSeqinfo' a list of lists containing the sequence info.

_N_o_t_e:

_A_u_t_h_o_r(_s):

     Kasper Daniel Hansen <khansen@stat.berkeley.edu>

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

     'tpmap2bpmap' for information on how to write Bpmap files.

_E_x_a_m_p_l_e_s:

