writeGFF3                package:reb                R Documentation

_O_u_t_p_u_t _o_f _a _G_F_F _c_o_m_p_l_i_a_n_t _t_a_b_l_e _d_e_s_c_r_i_b_i_n_g _t_h_e _e_n_h_a_n_c_e_d _a_n_d _d_i_m_i_n_i_s_h_e_d _c_h_r_o_m_o_s_o_m_a_l _b_a_n_d_s.

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

     This function writes out a GFF compliant tab delimited file for
     intergration with genome browsers.

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

     writeGFF3(cset, genome, chr, file.prefix = "temp.gff", organism = NULL)

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

    cset: expression set containing cytogenetic predictions, see 'reb'  

  genome: chromLocation object containing annotation information 

     chr: chromosome to examine 

file.prefix: character string - name of the output file, defaults to
          "temp.gff" 

organism: if NULL, determination of the host organism will be retrieved
          from the 'organism' slot of the chromLocation object.
          Otherwise '"h"', '"r"', or '"m"' can be used to specify
          *h*uman, *r*at, or *m*ouse chromosome information

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

     'writeGFF3' returns an invisible list of character vectors.

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

     Karl J. Dykema, karl.dykema@vai.org  Kyle A. Furge,
     kyle.furge@vai.org

_R_e_f_e_r_e_n_c_e_s:

     Furge KA, Dykema KJ, Ho C, Chen X. Comparison of array-based
     comparative genomic hybridization with gene expression-based
     regional expression biases to identify genetic abnormalities in
     hepatocellular carcinoma. BMC Genomics. 2005 May 9;6(1):67. PMID:
     1588246

     MCR eset data was obtained with permission. See PMID: 15377468

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

     'reb'

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

     data(idiogramExample)
     ix <- abs(colo.eset) > .225
     colo.eset[ix] <- NA
     idiogram(colo.eset,ucsf.chr,"14",method="i",dlim=c(-1,1),col=.rwb)
     gffmat <- writeGFF3(colo.eset,ucsf.chr,"14",NULL)
     gffmat[1:4,]

