fillPeaks.chrom-methods         package:xcms         R Documentation

_I_n_t_e_g_r_a_t_e _a_r_e_a_s _o_f _m_i_s_s_i_n_g _p_e_a_k_s

_D_e_s_c_r_i_p_t_i_o_n:

     For each sample, identify peak groups where that sample is not
     represented. For each of those peak groups, integrate the signal
     in the region of that peak group and create a new peak.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsSet' object

_D_e_t_a_i_l_s:

     After peak grouping, there will always be peak groups that do not
     include peaks from every sample. This method produces intensity
     values for those missing samples by integrating raw data in peak
     group region. In a given group, the start and ending retention
     time points for integration are defined by the median start and
     end points of the other detected peaks. The start and end m/z
     values are similarly determined. Intensities can be still be zero,
     which is a rather unusual intensity for a peak. This is the case
     if e.g. the raw data was threshholded, and the integration area
     contains no actual raw intensities, or if one sample is
     miscalibrated, such thet the raw data points are (just) outside
     the integration area.

     Importantly, if retention time correction data is available, the
     alignment information is used to more precisely integrate the
     propper region of the raw data. If the corrected retention time is
     beyond the end of the raw data, the value will be not-a-number
     (NaN).

_V_a_l_u_e:

     A 'xcmsSet' objects with filled in peak groups.

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_S_e_t" 'fillPeaks.chrom(object)'


_S_e_e _A_l_s_o:

     'xcmsSet-class', 'getPeaks' 'fillPeaks'

