readDcpRectangle {dChipIO}

Reads a spatial subset of probe-level data from a dChip DCP file

Description

Reads a spatial subset of probe-level data from a dChip DCP file.

Usage

readDcpRectangle(filename, fields=c("rawIntensities", "normalizedIntensities"),
  xrange=c(0, Inf), yrange=c(0, Inf), ..., asMatrix=TRUE)

Arguments

filename

The pathname of the DCP file.

fields

The cell fields to be read.

xrange

A numeric vector of length two giving the left and right coordinates of the cells to be returned.

yrange

A numeric vector of length two giving the top and bottom coordinates of the cells to be returned.

asMatrix

If TRUE, the CEL data fields are returned as matrices with element (1,1) corresponding to cell (xrange[1],yrange[1]).

...

Additional arguments passed to readDcp().

Value

A named list CEL structure similar to what readDcp(). In addition, if asMatrix is TRUE, the CEL data fields are returned as matrices, otherwise not.

Author(s)

Henrik Bengtsson

See Also

The readDcp() method is used internally. This method was inspired by readCelRectangle() of the affxparser package.

Examples

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

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

data <- readDcpRectangle(pathname)

layout(matrix(1:4, nrow=2, byrow=TRUE))
image(data$rawIntensities, main="Raw probe signals")
image(data$normalizedIntensities, main="Normalized probe signals")