readCdfNbrOfCellsPerUnitGroup {affxparser} | R Documentation

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

### Description

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

### Usage

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

### Arguments

`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.

### Value

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.

### Author(s)

Henrik Bengtsson

### Examples

    ##############################################################
    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 #
    ##############################################################

[Package affxparser version 1.56.0 Index]