bcrank                package:BCRANK                R Documentation

_B_C_R_A_N_K: _p_r_e_d_i_c_t_i_n_g _b_i_n_d_i_n_g _s_i_t_e _c_o_n_s_e_n_s_u_s _f_r_o_m _r_a_n_k_e_d _D_N_A _s_e_q_u_e_n_c_e_s

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

     This function implements an algorithm for detection of short DNA
     sequences that are overrepresented in some part of the list.
     Starting from some initial consensus DNA sequence coded in IUPAC
     symbols, the method uses a heuristic search to improve the
     consensus until a local optimum is found.

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

     bcrank(fafile, startguesses=c(), restarts=10, length=10, 
         reorderings=500, silent=FALSE, plot.progress=FALSE, do.search=TRUE)

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

  fafile: a ranked fasta file containing DNA sequences.

startguesses: a character vector with consensus sequences in IUPAC
          coding to be used as starting sequences in the search. If
          empty, random start guesses will be generated.

restarts: number restarts of the algorithm when using random start
          guesses.

  length: legth of random start guess.

reorderings: number of random reorderings of the DNA sequences
          performed when calculating score.

  silent: reports progress status if FALSE. 

plot.progress: if TRUE, the progress is displayed in a plot.

do.search: if FALSE, no search is performed. In that case the start
          guesses are assigned with scores and reported as results.

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

     The method returns an objcet of class 'BCRANKresult-class'.

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

     Adam Ameur, adam.ameur@lcb.uu.se

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

     Ameur, A., Rada-Iglesias, A., Komorowski, J., Wadelius, C. Novel
     algorithm and ChIP-analysis identifies candidate functional SNPs.
     Submitted

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

     'BCRANKresult-class'

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

     ## Load example fasta file  
     fastaFile <- system.file("Exfiles/USF1_small.fa", package = "BCRANK") 
     ## Run BCRANK
     ## Not run: BCRANKout <- bcrank(fastaFile, restarts=20)

     ## Show BCRANK results
     toptable(BCRANKout)
     ## The top scoring result
     topMotif <- toptable(BCRANKout,1)
     ## Plot BCRANK search path
     plot(topMotif)
     ## Position Weight Matrix
     pwm(topMotif, normalize=FALSE)

