ramp                  package:xcms                  R Documentation

_H_i_g_h-_p_e_r_f_o_r_m_a_n_c_e, _l_o_w-_l_e_v_e_l _a_c_c_e_s_s _t_o _m_z_X_M_L/_m_z_D_a_t_a _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Functions for low-level access to data in mzXML/mzData files. They
     have been optimized for maximum speed and memory efficiency.

_U_s_a_g_e:

     rampInit()
     rampPrintFiles()
     rampIsFile(filename)
     rampOpen(filename)
     rampClose(rampid)
     rampCloseAll()
     rampNumScans(rampid)
     rampScanHeaders(rampid)
     rampSIPeaks(rampid, seqNum, peaksCount)
     rampRawData(rampid)

_A_r_g_u_m_e_n_t_s:

filename: path to mxXML/mzData file

  rampid: RAMP file ID

  seqNum: integer vector with indecies of scans to read

peaksCount: integer vector with number of peaks in each scan to read 

_D_e_t_a_i_l_s:

     The mechanisms and structure of mzXML/mzData files are not
     discussed here, please see the mzXML/mzData documentation for more
     information. These functions make use of the RAMP (Random Access
     Minimal Parser) code from the SASHIMI open-source project.

     'rampInit' initializes the data structures used for holding RAMP
     file pointers and indices.

     'rampPrintFiles' prints out a list of all files currently open.

     'rampCloseAll' closes all mzXML/mzData files and frees memory
     associated with their indices.

_V_a_l_u_e:

     'rampIsFile' returns 'TRUE' if the referenced file is an mzXML or
     mzData file and 'FALSE' otherwise.

     'rampOpen' returns the 'rampid' of the opened file.

     'rampClose' returns the closing status.

     'rampNumScans' returns the number of scans with an msLevel of 1.

     'rampSIPeaks' returns a named list with components 'scanindex',
     'mz', and 'intensity'.

     'rampScanHeaders' returns a data frame with header information for
     each scan.

     'rampRawData' returns a named list with components 'rt', 'tic',
     'scanindex', 'mz', and 'intensity'.

     An error in any of the functions will return a (negative) integer
     error code.

_A_u_t_h_o_r(_s):

     Colin A. Smith, csmith@scripps.edu

_R_e_f_e_r_e_n_c_e_s:

     mzXML file format: <URL:
     http://sashimi.sourceforge.net/software_glossolalia.html>

     mzData file format: <URL:
     http://psidev.sourceforge.net/ms/index.html>

