BASHCompact            package:beadarray            R Documentation

_B_A_S_H - _C_o_m_p_a_c_t _D_e_f_e_c_t _A_n_a_l_y_s_i_s

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

     Creates a list of probes marked as being in compact defects.

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

     BASHCompact(BLData, array, neighbours = NULL, log = TRUE, maxiter = 10, cutoff = 8, cinvasions = 10, ...)

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

  BLData: 'BeadLevelList'

   array: integer specifying which strip/array to plot

neighbours: A Neighbours matrix. Optional - if left NULL, it will be
          computed.

     log: Logical - If TRUE, find outliers on the log scale.

 maxiter: Integer - Maximum number of iterations.

  cutoff: Integer - Size a cluster must be to be labelled a compact
          defect.

cinvasions: Integer - Number of invasions used when closing the image.

     ...: Additional arguments to be passed to 'findAllOutliers' (e.g.
          'what = "R"')

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

     'BASHCompact' finds "compact defects" on an array. A compact
     defect is defined as a large connected cluster of outliers.

     This function first finds the outliers on an array. This is done
     via the function 'findAllOutliers'.

     Next, using the Neighbours matrix and a Flood Fill algorithm, it
     determines which beads are in large connected clusters of outliers
     (of size larger than 'cutoff'). These beads are then temporarily
     removed and the process repeated with the remaining beads. The
     repetition continues until either no large clusters of outliers
     remain, or until we have repeated the process 'maxiter' times (and
     in this case, a warning will be given). In this way, we obtain a
     list of defective probes.

     Finally, we "close" the image, to fill in small gaps in the defect
     image. This consists of a "dilation" and an "erosion". In the
     dilation, we expand the defect image, by adding beads adjacent to
     defective beads into the defect image. This is repeated
     'cinvasions' times. In the erosion, we contract the defect image,
     by removing beads adjacent to non-defective beads from the defect
     image. (Erosion of the defect image is equivalent to a dilation of
     the non-defective image.)

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

     A vector consisting of the BeadIDs of beads labelled as compact
     defects.

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

     Jonathan Cairns

_R_e_f_e_r_e_n_c_e_s:

     Mayte Suarez-Farinas, Maurizio Pellegrino, Knut M. Wittkwosky and
     Marcelo O. Magnasco (2007). Harshlight: A "corrective make-up"
     program for microarray chips. R package version 1.8.0.
     http://asterion.rockefeller.edu/Harshlight/

_S_e_e _A_l_s_o:

     'BASHDiffuse', 'generateE', 'generateNeighbours',

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

     data(BLData)
     o <- BASHCompact(BLData, 1)
     o <- BASHCompact(BLData, 1, cinvasions = 10) ##increased no of closure invasions
     o <- BASHCompact(BLData, 1, cutoff = 12) ##only larger defects will be found with this setting

