AssociateWithInterval       package:AffyTiling       R Documentation

_R_e_t_u_r_n_s _i_n_d_e_x _o_f _a_s_s_o_c_i_a_t_i_o_n _b_e_t_w_e_e_n _a _p_r_o_b_e _a_n_d _a _s_e_t _o_f _g_e_n_o_m_i_c _i_n_t_e_r_v_a_l_s.

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

     Takes four vectors representing a unique ID, chromosome, start,
     and end of non-overlapping regions of interest (e.g. known genes,
     CpG islands, etc.).  Two additional vectors representing the
     chromosome and start position of probes in a tiling array.  

     One additional argument (optional) specifies the length of the
     probes.  This can be either a vector with one length for each
     probe, or a scalar if all probes are the same length.  If this
     argument is not specified, probes are assumed to be 25bp in
     length.

     Returns a vector representing the unique ID of the interval in
     which each probe can be found.  Values of NA are returned for
     probes that are located in any of the given genomic intervals.

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

     AssociateWithInterval(fID, fCHR, fSTART, fEND, pCHR, pSTART, pLENGTH)

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

     fID: Vector of unique IDs, representing each interval searched. 

    fCHR: Vector of chromosomes, one for each interval searched. 

  fSTART: Vector of start positions, one for each interval searched. 

    fEND: Vector of end positions, one for the each interval searched. 

    pCHR: Vector of chromosomes, one for each probes being annotated. 

  pSTART: Vector of start positions, one for each of the probes being
          annotated.  

 pLENGTH: Vector or scalar representing probe length.  Default is 25bp
          for each probe. 

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

     Charles Danko

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

     data(KnownGenes)

     ## Returns probes that fall inside known genes.
     Interval <- AssociateWithInterval( KG[,1], KG[,2], KG[,4], KG[,5], Einter[,3], as.integer(Einter[,2]) )

