findSequenceInGenome     package:GeneRegionScan     R Documentation

_F_i_n_d _a _s_e_q_u_e_n_c_e _i_n _g_e_n_o_m_e

_D_e_s_c_r_i_p_t_i_o_n:

     Wrapper around matchPDict that will accept a list of sequences and
     check if they are present in a given genome. Takes a long time to
     run.

_U_s_a_g_e:

         findSequenceInGenome(sequences, genome="BSgenome.Hsapiens.UCSC.hg18", verbose=TRUE,
         directions=c("matchForwardSense", "matchForwardAntisense", "matchReverseSense", "matchReverseAntisense"))

_A_r_g_u_m_e_n_t_s:

sequences: vector of character strings to scan. Should only contain A,
          C, G and T. Will be converted to DNAString.

  genome: character string with the name of the BSGenome in which
          sequences should be found. Defaults to the human genome.

 verbose: TRUE or FALSE.

directions: character string with elements from c("matchForwardSense",
          "matchForwardAntisense", "matchReverseSense",
          "matchReverseAntisense"). Defines which directions
          (complementary and reverse mirrorings) that should be
          scanned. Defaults to all directions.

_D_e_t_a_i_l_s:

     This function will take quite a while to run, so if you have a
     many sequences, overnight runs are recommended. BSgenome contains
     some alternative versions of chromosomes. They are marked with an
     underscore. This function automatically disregards chromosome
     names with an underscore, and this is known to work for the human
     genome. Nevertheless, check the output printed to terminal if all
     chromosomes are included.

_V_a_l_u_e:

     A data frame with a row for each identified match. Columns are
     "entrynumber","hitposInChr","chr", and "sequence" describing,
     respectively: the index of the sequence match, the position in the
     chromosome at which it was found, which chromosome it was found
     on, the sequence itself

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'BSgenome', 'matchPDict', 'excludeDoubleMatchingProbes'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             #you can run this, but it takes quite a lot of time
             example<-findSequenceInGenome("CTGGCGAGCAGCGAATAATGGTTT")
             
     ## End(Not run)

