profRange-methods            package:xcms            R Documentation

_S_p_e_c_i_f_y _a _s_u_b_s_e_t _o_f _p_r_o_f_i_l_e _m_o_d_e _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Specify a subset of the profile mode matrix given a mass, time, or
     scan range. Allow flexible user entry for other functions.

_A_r_g_u_m_e_n_t_s:

  object: the 'xcmsRaw' object

massrange: single numeric mass or vector of masses

timerange: single numeric time (in seconds) or vector of times 

scanrange: single integer scan index or vector of indecies

     ...: arguments to other functions

_D_e_t_a_i_l_s:

     This function handles selection of mass/time subsets of the
     profile matrix for other functions. It allows the user to specify
     such subsets in a variety of flexible ways with minimal typing.

     Because R does partial argument matching, 'massrange',
     'scanrange', and 'timerange' can be specified in short form using
     'm=', 's=', and 't=', respectively. If both a 'scanrange' and
     'timerange' are specified, then the 'timerange' specification
     takes precedence.

     When specifying ranges, you may either enter a single number or a
     numeric vector. If a single number is entered, then the closest
     single scan or mass value is selected. If a vector is entered,
     then the range is set to the 'range()' of the values entered. That
     allows specification of ranges using shortened, slightly
     non-standard syntax. For example, one could specify 400 to 500
     seconds using any of the following: 't=c(400,500)',
     't=c(500,400)', or 't=400:500'. Use of the sequence operator (':')
     can save several keystrokes when specifying ranges. However, while
     the sequence operator works well for specifying integer ranges,
     fractional ranges do not always work as well.

_V_a_l_u_e:

     A list with the folloing items:

massrange: numeric vector with start and end mass

 masslab: textual label of mass range

 massidx: integer vector of mass indecies

scanrange: integer vector with stat ane end scans

 scanlab: textual label of scan range

 scanidx: integer vector of scan range

timerange: numeric vector of start and end times

 timelab: textual label of time range

_M_e_t_h_o_d_s:


     _o_b_j_e_c_t = "_x_c_m_s_R_a_w" 'profRange(object, massrange = numeric(),
          timerange = numeric(), scanrange = numeric(), ...)'


_S_e_e _A_l_s_o:

     'xcmsRaw-class'

