readCdfBin: Reads a dChip CDF.bin file

In dChipIO: Methods for reading dChip files

Description

Reads a dChip CDF.bin file.

Please note that this method is incomplete as it currently doesn't read all fields. It is only made available so that someelse can continue the development.

Usage

readCdfBin(con, units=NULL, ...)

Arguments

con	A connection or a character filename.
units	An integer vector specifying the units to be read. If NULL, all units are read.
...	Not used.

Value

Returns a list structure containing the file header and the unit data.

Author(s)

Henrik Bengtsson

See Also

To read only the CDF.bin file header, see readCdfBinHeader().

Examples

path <- system.file("exData", package="dChipIO")
chipType <- "Test3"
filename <- sprintf("%s.CDF.bin", chipType)
pathname <- file.path(path, filename)

hdr <- readCdfBinHeader(pathname)
print(hdr)

data <- readCdfBin(pathname)
str(data)

# Read a subset of the units
units <- c(10:11, 15:20, 150:105, 2,2,2)
dataT <- readCdfBin(pathname, units=units)
str(dataT)

# Assert correctness
for (ff in c("unitNames", "numProbes", "CellPos")) {
  stopifnot(length(dataT[[ff]]) == length(units))
  stopifnot(identical(dataT[[ff]], data[[ff]][units]))
}

Example output

dChipIO v0.1.5 (2016-01-12) successfully loaded. See ?dChipIO for help.
$FileName
[1] "C:\\Documents and Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\annotationData\\Test3.CDF.bin"

$Format
[1] 4

$ChipType
[1] "Test3"

$CellDim
[1] 126

$NumUnit
[1] 345

List of 4
 $ header   :List of 5
  ..$ FileName: chr "C:\\Documents and Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\annotationData\\Test3.CDF.bin"
  ..$ Format  : int 4
  ..$ ChipType: chr "Test3"
  ..$ CellDim : int 126
  ..$ NumUnit : int 345
 $ unitNames: chr [1:345] "Pae_16SrRNA_s_at" "Pae_23SrRNA_s_at" "PA1178_oprH_at" "PA1816_dnaQ_at" ...
 $ numProbes: int [1:345] 32 32 24 24 24 24 24 32 32 24 ...
 $ CellPos  : int [1:345] 0 0 0 0 0 0 0 0 0 0 ...
List of 4
 $ header   :List of 5
  ..$ FileName: chr "C:\\Documents and Settings\\hb\\braju.com.R\\aroma.affymetrix\\reengineeringdChip\\annotationData\\Test3.CDF.bin"
  ..$ Format  : int 4
  ..$ ChipType: chr "Test3"
  ..$ CellDim : int 126
  ..$ NumUnit : int 345
 $ unitNames: chr [1:57] "PA1178_oprH_st" "PA1816_dnaQ_st" "AFFX-Athal-Actin_5_r_at" "AFFX-Athal-Actin_M_at" ...
 $ numProbes: int [1:57] 24 24 32 32 32 32 32 32 32 32 ...
 $ CellPos  : int [1:57] 0 0 0 0 0 0 0 0 0 0 ...

dChipIO documentation built on May 2, 2019, 5:25 p.m.