readDcp: Reads a dChip DCP file
In HenrikBengtsson/dChipIO: Methods for Reading dChip Files

Description Usage Arguments Value Author(s) See Also Examples

Reads a dChip DCP file.

1 2	readDcp(con, fields=c("rawIntensities", "normalizedIntensities", "calls", "thetas", "thetaStds", "excludes"), cells=NULL, units=NULL, .nbrOfUnits=NULL, ...)

`con`	A `connection` or a `character` filename.
`fields`	A `character` `vector` specifying the fields to be read.
`cells`	An `integer` `vector` specifying the indices of the cell data to be read.
`units`	An `integer` `vector` specifying the indices of the unit data to be read.
`.nbrOfUnits`	A `integer` specifying the number of units available in the file. If `NULL`, this is inferred from the file size and the file header. The dChip software itself instead uses the corrsponding value in the CDF.bin file, but that file is specified by the user leaving room for errors.
`...`	Not used.

Returns a list structure containing the file header and the requested data fields.

Henrik Bengtsson

To read only the DCP file header, see readDcpHeader().

path <- system.file("exData", package="dChipIO")

filename <- "Test3-1-121502.dcp"
pathname <- file.path(path, filename)

hdr <- readDcpHeader(pathname)
print(hdr)

data <- readDcp(pathname)
str(data)

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

# Assert correctness
for (ff in c("calls", "thetas", "thetaStds", "excludes")) {
  stopifnot(length(dataT[[ff]]) == length(units))
  stopifnot(identical(dataT[[ff]], data[[ff]][units]))
}