addAMDISPeaks             package:flagme             R Documentation

_A_d_d _A_M_D_I_S _p_e_a_k _d_e_t_e_c_t_i_o_n _r_e_s_u_l_t_s

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

     Reads ASCII ELU-format files (output from AMDIS) and attaches them
     to an already created 'peaksDataset' object

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

     addAMDISPeaks(object,fns=dir(,"[Eu][Ll][Uu]"),verbose=TRUE,...)

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

  object: a 'peaksDataset' object.

     fns: character vector of same length as 'object@rawdata' (user
          ensures the order matches)

 verbose: whether to give verbose output, default 'TRUE'

     ...: arguments passed on to 'parseELU'

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

     Repeated calls to 'parseELU' to add peak detection results to the
     original 'peaksDataset' object.

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

     'peaksDataset' object

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

     Mark Robinson

_R_e_f_e_r_e_n_c_e_s:

     Mark D Robinson (2008).  Methods for the analysis of gas
     chromatography - mass spectrometry data  _PhD dissertation_
     University of Melbourne.

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

     'parseELU', 'peaksDataset'

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

     # need access to CDF (raw data) and ELU files 
     require(gcspikelite)
     gcmsPath<-paste(.find.package("gcspikelite"),"data",sep="/")

     # full paths to file names
     cdfFiles<-dir(gcmsPath,"CDF",full=TRUE)
     eluFiles<-dir(gcmsPath,"ELU",full=TRUE)

     # create a 'peaksDataset' object and add AMDIS peaks to it
     pd<-peaksDataset(cdfFiles[1],mz=seq(50,550),rtrange=c(7.5,8.5))
     pd<-addAMDISPeaks(pd,eluFiles[1])

