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'

