faahko                package:faahKO                R Documentation

_F_A_A_H _k_n_o_c_k_o_u_t _L_C/_M_S _d_a_t_a _x_c_m_s_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     'xcmsSet' object containing quantitated LC/MS peaks from the
     spinal cords of 6 wild-type and 6 FAAH knockout mice. The data is
     a subset of the original data from 200-600 m/z and 2500-4500
     seconds. It was collected in positive ionization mode.

_U_s_a_g_e:

     data(faahko)

_F_o_r_m_a_t:

     The format is:  
     Formal class 'xcmsSet' [package "xcms"] with 8 slots
       ..@ peaks    : num [1:4776, 1:11] 200 201 205 206 207 ...
       ..@ groups   : logi[0 , 0 ] 
       ..@ groupidx : list()
       ..@ sampnames: chr [1:12] "ko15" "ko16" "ko18" "ko19" ...
       ..@ sampclass: Factor w/ 2 levels "KO","WT": 1 1 1 1 1 1 2 2 2 2
     ...
       ..@ rt       :List of 2
       .. ..$ raw      :List of 12
       .. ..$ corrected:List of 12
       ..@ cdfpaths : chr [1:12] ...
       ..@ profinfo :List of 2
       .. ..$ method: chr "bin"
       .. ..$ step  : num 0.1


_D_e_t_a_i_l_s:

     The corresponding raw NetCDF files are located in the 'cdf'
     subdirectory of this package.

_S_o_u_r_c_e:

     <URL: http://dx.doi.org/10.1021/bi0480335>

_R_e_f_e_r_e_n_c_e_s:

     Saghatelian A, Trauger SA, Want EJ, Hawkins EG, Siuzdak G, Cravatt
     BF. Assignment of endogenous substrates to enzymes by global
     metabolite profiling. _Biochemistry_. 2004 Nov 16;43(45):14332-9.

_S_e_e _A_l_s_o:

     'xcmsSet', 'xcmsRaw'

_E_x_a_m_p_l_e_s:

     ## The directory with the NetCDF LC/MS files
     cdfpath <- file.path(.find.package("faahKO"), "cdf")
     cdfpath
     list.files(cdfpath, recursive = TRUE)

     if (require(xcms)) {

     ## xcmsSet Summary
     show(faahko)

     ## Access raw data file
     ko15 <- xcmsRaw(cdfpaths(faahko)[1], profmethod = "bin", profstep = 0.1)
     ko15

     }

