ArrayMask             package:beadarray             R Documentation

_A_r_r_a_y _M_a_s_k

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

     Functions to edit or display array masks.

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

     addArrayMask(BLData, array, SAM = FALSE, nrow = 50, ncol = 50, high = "red",
             low = "yellow", zlim = c(7,15), override = FALSE)
     removeArrayMask(BLData, array, SAM = FALSE, nrow = 50, ncol = 50, high = "red",
             low = "yellow", zlim = c(7,15), override = FALSE)
     showArrayMask(BLData,array, SAM = FALSE, elim = TRUE, override = FALSE)
     clearArrayMask(BLData,array)

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

  BLData: A BeadLevelList object.

   array: The number of an array in the BeadLevelList object.

     SAM: Logical. If 'TRUE', display a hexagonal overlay where
          appropriate.

    elim: Logical. If TRUE, plot eliminated beads (with blue crosses).

nrow, ncol, high, low, zlim: Arguments passed to 'imageplot' - see the
          help for 'imageplot' for details.

override: Logical. Plotting a large mask can cause slowdown problems.
          By default, if more than 200 000 beads are masked, the
          current mask will not be plotted. You can force the mask to
          be plotted by setting this argument to 'TRUE', however beware
          as this may cause slower systems to freeze.

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

     These functions are used to manipulate the mask on a single array.

     'addArrayMask' adds beads in a specified region to the mask (i.e.
     sets their weights to 0).

     'removeArrayMask' removes beads in a specified region from the
     mask (i.e. sets their weights to 0)

     On calling either of these functions, an imageplot is displayed.
     Click on the plot to define vertices of a polygon, in order.
     Having specified the last vertex, right-click to close the
     polygon. A plot is then produced of the beads currently masked on
     the array (in grey) and the polygon just defined (in red), with a
     menu prompting you to accept the displayed region - if you do so,
     then all beads in the polygon then be masked or unmasked as
     appropriate. Alternatively, you can right-click on the image
     without defining any vertices, thus leaving the mask unchanged. 

     If making the change would result in all beads of a certain probe
     ID being completely covered by the mask, then the functions return
     a warning message, and the beads eliminated in this way are
     highlighted with blue crosses on the plot.

     'showArrayMask' plots the beads on an array which have been
     masked, over a plot of outliers.

     'clearArrayMask' clears the mask on an array, removing all weights
     associated with it.

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

     None returned

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

     Jonathan Cairns

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

     'listEliminatedProbes'

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

     ##data(BLData)
     ##addArrayMask(BLData,1)
     ##showArrayMask(BLData,1)

