matchingSites             package:BCRANK             R Documentation

_R_e_p_o_r_t _I_U_P_A_C _c_o_n_s_e_n_s_u_s _o_c_c_u_r_r_e_n_c_e_s _i_n _a _f_a_s_t_a _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function reports all occurrences of a consensus sequence in a
     fasta file. It can be used to extract transcription factor binding
     sites predicted by BCRANK or other motif search methods.

_U_s_a_g_e:

     matchingSites(fafile, motifSequence, revComp=TRUE, strip.desc=TRUE)

_A_r_g_u_m_e_n_t_s:

  fafile: a ranked fasta file containing DNA sequences.

motifSequence: a character vector in IUPAC coding representing a DNA
          sequence.

 revComp: set to TRUE if the reverse complement also be matched.

strip.desc: An argument used by the function 'readFASTA()'. It
          specifies whether or not the ">" marking at the beginning of
          description lines should be removed.

_V_a_l_u_e:

     Returns a data frame with positions, strand and DNA sequence for
     the matching sites.

_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:

     'bcrank'

