read.resultsGFF             package:ACME             R Documentation

_R_e_a_d _N_i_m_b_l_e_g_e_n _G_F_F _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A GFF format file is a quite flexible format for storing genomic
     data.  Nimblegen uses these format files as one format for making
     chip-chip data available.  This function reads these files, one
     per experiment and creates a resulting aGFF-class object.

_U_s_a_g_e:

     read.resultsGFF(fnames, path = NULL, samples = NULL, notes = NULL, skip = 0, sep = "\t", quote = "\"", ...)

_A_r_g_u_m_e_n_t_s:

  fnames: A vector of filenames

    path: The path to the filenames or 'NULL' for relative to the local
          directory

 samples: A data.frame containing sample information, one row per
          sample, in the same order as the files in fnames

   notes: A character vector for notes-not currently stored

    skip: Number of lines to skip if the file contains a header

     sep: The field separator-should be a tab character for gff files,
          but can be set if necessary.

   quote: The text quote character-again not used for gff file,
          typically

     ...: ...

_D_e_t_a_i_l_s:

     The output is an aGFF object.

_V_a_l_u_e:

     A single aGFF object.

_A_u_t_h_o_r(_s):

     Sean Davis <sdavis2@mail.nih.gov>

_R_e_f_e_r_e_n_c_e_s:

     http://www.sanger.ac.uk/Software/formats/GFF/

_S_e_e _A_l_s_o:

     'aGFF-class'

_E_x_a_m_p_l_e_s:

     datdir <- system.file('extdata',package='ACME')
     fnames <- dir(datdir)
     example.agff <- read.resultsGFF(fnames,path=datdir)

