revish                  package:reb                  R Documentation

_C_r_e_a_t_i_o_n _o_f _C_G_H (_r_e_v_e_r_s_e _i_n _s_i_t_u _h_y_b_r_i_d_i_z_a_t_i_o_n) _s_t_y_l_e _c_h_a_r_a_c_t_e_r _s_t_r_i_n_g_s

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

     This function returns a two lists of character strings. These two
     lists correspond to  the enhanced and diminished chromosomal
     bands.

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

     revish(cset, genome, chr, 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 

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:

    enh : list of enhanced bands on each individual sample

    dim : list of diminished bands on each individual sample

_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)
     revlist<- revish(colo.eset,ucsf.chr,"14")
     str(revlist)

