fromRevIsh                package:reb                R Documentation

_C_o_n_v_e_r_t _f_r_o_m _r_e_v_i_s_h _s_t_r_i_n_g_s _t_o _a _m_a_t_r_i_x

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

     This function will convert two lists of revish style strings to a
     matrix format.

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

     fromRevIsh(enhList, dimList, chr, organism = "h")

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

 enhList: list of enhanced bands on each individual sample 

 dimList: list of diminished bands on each individual sample 

     chr: chromosome to examine 

organism: character, "h" for human, "m" for mouse, and "r" for rat.

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

     A matrix is returned. The rownames of this matrix correspond to
     the major bands located on that chromosome,  and the columns
     correspond to the sample names.

_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:

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

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

     'reb','revish'

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

     mb.chr <- buildChromCytoband("h")

     data(mcr.eset)
     data(idiogramExample)
             ## Create a vector with the index of normal samples
     norms <- grep("MNC",colnames(mcr.eset@exprs))
             ## Smooth the data using the default 'movbin' method, with the normal samples as reference and median centering
     cset <- reb(mcr.eset@exprs,vai.chr,ref=norms,center=TRUE)
             ## Mask the cset to remove noise
     exprs <- cset[,-norms]
     exprs[abs(exprs) < 1.96] <- NA
             ## Extract the aberrations on the 5th chromosome
     revish <- revish(exprs,vai.chr,"5")
             ## Convert back to matrix
     reconverted <- fromRevIsh(revish[[1]],revish[[2]],"5")

     layout(cbind(1,2))
     idiogram(cset[,-norms],vai.chr,"5",method="i",dlim=c(-2,2),col=.rwb,main="chr 5 reb results")
     idiogram(reconverted,mb.chr,"5",method="i",dlim=c(-1,1),col=.rwb,main="chr 5 converted \n and re-converted")

             

