findClosestGene             package:ACME             R Documentation

_F_i_n_d _c_l_o_s_e_s_t _r_e_f_s_e_q _g_e_n_e

_D_e_s_c_r_i_p_t_i_o_n:

     This function is used to find the nearest refseq transcript(s) to
     a point in the genome specified.  Note that it is limited to the
     refseq transcripts listed at genome.ucsc.edu, where this function
     goes for information.

_U_s_a_g_e:

     findClosestGene(chrom, pos, genome = "hg17", position = "txStart")

_A_r_g_u_m_e_n_t_s:

   chrom: Usually specified like 'chr1', 'chr2', etc. 

     pos: A position in base pairs in the genome 

  genome: Something like 'hg16', 'hg17', 'mm6', etc. 

position: The location to measure distance from: one of 'txStart',
          'txEnd', 'cdsStart', 'cdsEnd'

_D_e_t_a_i_l_s:

     The first time the function is run, it checks to see if the
     refflat table for the given genome is present in the package
     environment.  If not, it downloads it to the /tmp directory and
     gunzips it (using getRefflat.  It is then stored so that in future
     calls, there is no re-download required.

_V_a_l_u_e:

     A data frame with the gene name, refseq id(s), txStart, txEnd,
     cdsStart, cdsEnd, exon count, and distance.  Note that distance is
     measured as pos-position, so negative values mean that the point
     in the gene is to the left of the point specified in the function
     call (with the p-tel on the left).

_N_o_t_e:

     The function may return more than one transcript, as several
     transcripts may have the same start site

_A_u_t_h_o_r(_s):

     Sean Davis <sdavis2@mail.nih.gov>

_E_x_a_m_p_l_e_s:

     findClosestGene('chr1',100000000,'hg17')

