browseGenome           package:rtracklayer           R Documentation

_B_r_o_w_s_e _a _g_e_n_o_m_e

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

     A generic function for launching a genome browser.

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

     browseGenome(object, ...)
     ## S4 method for signature 'RangedDataORRangedDataList':
     browseGenome(object = RangedDataList(),
       browser = "ucsc", range = range(tracks),
       view = TRUE, trackParams = list(), viewParams = list(), ...)

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

  object: A list of 'RangedData' instances, e.g. a 'RangedDataList'
          instance.

 browser: The name of the genome browser. 

   range: The 'RangesList' to display in the initial view. 

    view: Whether to open a view. 

trackParams: Named list of parameters to pass to 'track<-'. 

viewParams: Named list of parameters to pass to 'browserView'. 

     ...: Arguments corresponding to slots in 'RangesList' that
          override those in 'range'. 

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

     Returns a 'BrowserSession'.

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

     Michael Lawrence

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

     'BrowserSession' and 'BrowserView', the two main classes for
     interfacing with genome browsers.

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

       ## Not run: 
       ## open UCSC genome browser:
       browseGenome()
       ## to view a specific range:
       range <- GenomicRanges("hg18", "chr22", 20000, 50000)
       browseGenome(range = range)
       ## a slightly larger range:
       browseGenome(range = range, end = 75000)
       ## with a track:
       track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
       browseGenome(RangedDataList(track))
       
     ## End(Not run)

