exportCherList             package:Ringo             R Documentation

_F_u_n_c_t_i_o_n _t_o _e_x_p_o_r_t _c_h_e_r_L_i_s_t _i_n_t_o _a _f_i_l_e

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

     Function to export cherList into a file of gff or BED format. This
     files can be imported as tracks into genome browsers.

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

     exportCherList(object, filename = "chers.gff", format = "gff3", ...)

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

  object: an object of class 'cherList'

filename: character; path to file to be written

  format: Format of exported file; currently only "gff3" and "bed" are
          supported

     ...: further arguments to be passed on to the 'trackSet' method

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

     First converts the 'cherList' into an object of class 'trackSet'
     from package 'rtracklayer' and then calls the 'export' method as
     defined for a 'trackSet'.

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

     returns invisible NULL; called for the side effect of writing the
     file 'filename'.

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

     Joern Toedling

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

     Class 'trackset' in package 'rtracklayer'

_E_x_a_m_p_l_e_s:

     ## Not run: 
       exDir <- system.file("exData",package="Ringo")
       load(file.path(exDir,"exampleProbeAnno.rda"))
       load(file.path(exDir,"exampleX.rda"))
       smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
            modColumn = "Cy5", allChr = "9", winHalfSize = 400)
       chersX <- findChersOnSmoothed(smoothX, probeAnno=exProbeAnno,
            thresholds=0.45, allChr="9", distCutOff=600, cellType="human")
       exportCherList(chersX, file="chers.gff")
     ## End(Not run)

