ReadBPMAPAllSeqHeader          package:rMAT          R Documentation

_R_e_a_d_i_n_g _A_l_l _t_h_e _B_P_M_A_P _S_e_q_u_e_n_c_e _H_e_a_d_e_r

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

     Reading the header of a specified sequence in the BPMAP file.
     Several sequences could be stored in a single Affymetrix Tiling
     Array. For example, an array could contain probes from Chromosome
     21 and Chromosome 22. The sequenceNum uniquely specifies a
     sequence. Information about this sequence could be determined in
     this function. The total number of sequences a tiling array
     contains can be determined in ReadBPMAPHeader(fileName). The
     sequenceNum indexes from 0 to (total number of sequences -1).

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

     ReadBPMAPAllSeqHeader(fileName)

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

fileName: the full path of the BPMAP file to be read.

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

     The BPMAP Sequence Header gives information about the design of
     the tiling array.

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

     A list of vectors containing SeqName, GroupName, version,
     npnrobeMapping, seqNum, and NumHits.

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

     Charles Cheung, cykc@interchange.ubc.ca and Raphael Gottardo,
     raphael.gottardo@ircm.qc.ca Arnaud Droit, arnaud.droit@ircm.qc.ca

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

     'BPMAPCelParser()' for an one-step BPMAP/CEL parser and 'affyTile'
     for information about the package.

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

     ####################################################
     #The data are in inst/doc folder in rMAT package.
     ####################################################

     pwd<-"" #INPUT FILES- BPMAP, ARRAYS, etc.
     path<- system.file("doc/Sc03b_MR_v04_10000.bpmap",package="rMAT")

     bpmapFile<-paste(pwd,path,sep="")

     pathCEL<- system.file("doc/Swr1WTIP_Short.CEL",package="rMAT")
     arrayFile<-paste(pwd,c(pathCEL),sep="")

     # Show the all the different sequences
     ReadBPMAPAllSeqHeader(bpmapFile)

