FindPeaks            package:TargetSearch            R Documentation

_E_x_t_r_a_c_t _p_e_a_k_s _f_r_o_m _c_h_r_o_m_a_t_o_g_r_a_m _f_i_l_e_s

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

     This function extracts the maximum intensity of a list of masses
     in a given RI window.

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

     FindPeaks(my.files, refLib, columns = c("SPECTRUM", "RETENTION_TIME_INDEX"),
               showProgressBar = FALSE)

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

my.files: A character vector naming files to be searched. 

  refLib: A numeric matrix with three columns. The second column
          contains the masses and the first and third column contains
          the RI limits. 

 columns: A numeric vector with the positions of the columns 'SPECTRUM'
          and 'RETENTION_TIME_INDEX' or a character vector with the
          header names of those columns. 

showProgressBar: Logical. Should the progress bar be displayed?

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

     A 'tsMSdata' object.

_N_o_t_e:

     This is an internal function not intended to be invoked directly.

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

     Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

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

     'medianRILib', 'sampleRI',  'peakFind',  'tsMSdata'

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

     require(TargetSearchData)
     data(TargetSearchData)

     # get RI file path
     RI.path <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
     # update RI file path
     RIpath(sampleDescription) <- RI.path

     my.files <- RIfiles(sampleDescription)
     # make a three column matrix: lower RI, mass, upper RI
     refLib   <- refLib(refLibrary)
     head(refLib)

     # extract the peaks
     peaks <- FindPeaks(my.files, refLib)
         

