ImportFameSettings       package:TargetSearch       R Documentation

_R_e_t_e_n_t_i_o_n _t_i_m_e _m_a_r_k_e_r_s _s_e_t_t_i_n_g_s

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

     This function imports a list of retention standard markers.

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

     ImportFameSettings(tmp.file = NA, mass = NA, ...)

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

tmp.file: A character string naming a file with standard markers. 

    mass: The m/z standard marker. 

     ...: Other options passed to 'read.delim' function. 

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

     The standard marker file is a tab-delimited text file with 3
     columns. Column names doesn't matter. They must be in the
     following order.


        *  'LowerLimit' - The Retention time lower limit in seconds.

        *  'UpperLimit' - The Retention time upper limit in seconds.

        *  'RIstandard' - The RI value of that standard.

     If no arguments are given, a default object will be returned.

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

     A 'tsRim' object.

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

     Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

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

     'RIcorrect', 'tsRim'

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

     # get the RI marker definition file
     cdfpath  <- file.path(.find.package("TargetSearchData"), "gc-ms-data")
     rim.file <- file.path(cdfpath, "rimLimits.txt")

     # set the mass marker to 87
     mass <- 87

     # load the definition
     rimLimits <- ImportFameSettings(rim.file, mass = mass)

     # sometimes you need to change the limits of a particular standard
     rimLimits(rimLimits)[2,] <- c(410, 450)

     # to change the mass value
     rimMass(rimLimits) <- 85

