specNoise                package:xcms                R Documentation

_C_a_l_c_u_l_a_t_e _n_o_i_s_e _f_o_r _a _s_p_a_r_s_e _c_o_n_t_i_n_u_u_m _m_a_s_s _s_p_e_c_t_r_u_m

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

     Given a sparse continuum mass spectrum, determine regions where no
     signal is present, substituting half of the minimum intensity for
     those regions. Calculate the noise level as the weighted mean of
     the regions with signal and the regions without signal.

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

     specNoise(spec, gap = quantile(diff(spec[, "mz"]), 0.9))

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

    spec: matrix with named columns 'mz' and 'intensity'

     gap: threshold above which to data points are considerd to be
          separated by a blank region and not bridged by an
          interpolating line 

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

     The default gap value is determined from the 90th percentile of
     the pair-wise differences between adjacent mass values.

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

     A numeric noise level

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

     Colin A. Smith, csmith@scripps.edu

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

     'getSpec', 'specPeaks'

