readCdfNbrOfCellsPerUnitGroup   package:affxparser   R Documentation

_G_e_t_s _t_h_e _n_u_m_b_e_r _o_f _c_e_l_l_s (_p_r_o_b_e_s) _t_h_a_t _e_a_c_h _g_r_o_u_p _o_f _e_a_c_h _u_n_i_t _i_n _a _C_D_F _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Gets the number of cells (probes) that each group of each unit in
     a CDF file.

_U_s_a_g_e:

     readCdfNbrOfCellsPerUnitGroup(filename, units=NULL, verbose=0)

_A_r_g_u_m_e_n_t_s:

filename: The filename of the CDF file.

   units: An 'integer' 'vector' of unit indices specifying which units
          to be read.  If 'NULL', all units are read.

 verbose: An 'integer' specifying the verbose level. If 0, the file is
          parsed quietly.  The higher numbers, the more details.

_V_a_l_u_e:

     A named 'list' of named 'integer' vectors.  The name of the list
     elements are unit names and the names of the integer vector are
     group names.

_A_u_t_h_o_r(_s):

     Henrik Bengtsson (<URL: http://www.braju.com/R/>)

_E_x_a_m_p_l_e_s:

     ##############################################################
     if (require("AffymetrixDataTestFiles")) {            # START #
     ##############################################################

     cdfFile <- findCdf("Mapping10K_Xba131")

     groups <- readCdfNbrOfCellsPerUnitGroup(cdfFile)

     # Number of units read
     print(length(groups))
     ##   11564

     # Details on two units
     print(groups[56:57])
     ## $`SNP_A-1516438`
     ## SNP_A-1516438C SNP_A-1516438T SNP_A-1516438C SNP_A-1516438T
     ##             10             10             10             10
     ##
     ## $`SNP_A-1508602`
     ## SNP_A-1508602A SNP_A-1508602G SNP_A-1508602A SNP_A-1508602G
     ##             10             10             10             10

     # Number of groups with different number of cells
     print(table(unlist(groups)))
     ##    10    60
     ## 46240     4

     # Number of cells per unit
     nbrOfCellsPerUnit <- unlist(lapply(groups, FUN=sum))
     print(table(nbrOfCellsPerUnit))
     nbrOfCellsPerUnit
     ##    40    60
     ## 11560     4

     # Number of groups per unit
     nbrOfGroupsPerUnit <- unlist(lapply(groups, FUN=length))

     # Details on a few units
     print(nbrOfGroupsPerUnit[20:30])
     ## SNP_A-1512666 SNP_A-1512740 SNP_A-1512132 SNP_A-1516082 SNP_A-1511962
     ##             4             4             4             4             4
     ## SNP_A-1515637 SNP_A-1515878 SNP_A-1518789 SNP_A-1518296 SNP_A-1519701
     ##             4             4             4             4             4
     ## SNP_A-1511743
     ##             4

     # Number of units for each unique number of groups
     print(table(nbrOfGroupsPerUnit))
     ## nbrOfGroupsPerUnit
     ##     1     4
     ##     4 11560

     x <- list()
     for (size in unique(nbrOfGroupsPerUnit)) {
       subset <- groups[nbrOfGroupsPerUnit==size]
       t <- matrix(unlist(subset), nrow=size)
       colnames(t) <- names(subset)
       x[[as.character(size)]] <- t
       rm(subset, t)
     }

     # Check if there are any quartet units where the number
     # of cells in Group 1 & 2 or Group 3 & 4 does not have
     # the same number of cells.
     # Group 1 & 2
     print(sum(x[["4"]][1,]-x[["4"]][2,] != 0))
     # 0

     # Group 3 & 4
     print(sum(x[["4"]][3,]-x[["4"]][4,] != 0))
     # 0

     ##############################################################
     }                                                     # STOP #
     ##############################################################

