findLowestCounts          package:beadarray          R Documentation

_F_i_n_d _L_o_w_e_s_t _b_e_a_d _c_o_u_n_t_s

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

     Find bead types which are represented less than 24 times a given
     array

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

     findLowestCounts(BLData, array, limit = 24)

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

  BLData: BeadLevelList object containing bead level data

   array: numeric value for the array we are interested in

   limit: numeric value defining when bead types should be returned by
          the function

_D_e_t_a_i_l_s:

     It is known that the  numbers of each bead type on an array should
     be Poisson and on average around 30 of each bead type should be
     seen. This high amount of replication is  a major advantage of the
     BeadArray technology.

     The function simply loops through all the different ProbeIDs found
     on the array and counts how many of the bead type there are. If
     the number of beads found  is less than 'limit' then the bead type
     is added to a list which is returned by the function.

     The default value for 'limit' is 24 which is the 5th percentile of
     the appropriate Poisson distribution.

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

     numeric vector giving the ProbeIDs of the bead types which occur
     less than 'limit' times on the array.

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

     Mark Dunning

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

     data(BLData)

     ##Default is to find all bead types represented less than 24 times

     findLowestCounts(BLData, 1)

     ##Can change limit parameter to give all bead types represented less than 20 times

     findLowestCounts(BLData, 1, limit=20)

     ##ProbeIDs returned by function can be investigated in more detail

     plotBeadLocations(BLData, ProbeID=87, array=1)

