getMatrix              package:cellHTS              R Documentation

_C_r_e_a_t_e _a _m_a_t_r_i_x _w_i_t_h _r_e_p_l_i_c_a_t_e _d_a_t_a _i_n _c_o_l_u_m_n_s

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

     Given an array of raw or normalized intensities ('x$raw' or
     'x$xnorm'), creates a matrix with the data from the chosen
     channel.

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

     getMatrix(y, channel=1, na.rm=FALSE)

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

       y: an array with four dimensions, such as 'y=x$xraw' or
          'y=x$xnorm', where 'x' is a 'cellHTS' object.

 channel: a numeric value corresponding to the selected channel of 'y'.
          By default, the first channel (that is, 'y[,,,1]' is
          considered).

   na.rm: Logical, indicated if the missing values should be omitted.

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

     Given as input an array 'y' (e.g. the slot 'xraw', or 'xnorm' of a
     'cellHTS' object) with dimensions 'nr wells x nr plates x nr
     replicates x nr channels', this function creates a matrix with the
     data for the chosen 'channel'. Each replicate corresponds to a
     column of the output matrix. If 'na.rm' is set to 'TRUE', only the
     positions with available values for all the replicates are given
     in the output matrix.

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

     A matrix with the same number of columns as the number of
     replicates (third dimension of 'y'). If 'na.rm=FALSE' (the
     default), the number of rows of the output matrix is identical to
     the product between the first two dimensions of 'y' ('nr wells x
     nr plates'). If 'na.rm=TRUE', only the rows with no missing
     entries in all the replicates (columns) are given.

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

     Ligia Brás ligia@ebi.ac.uk

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

         data(KcViabSmall)
         y <- getMatrix(KcViabSmall$xraw)

