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

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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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

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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")

HenrikBengtsson/dChipIO documentation built on June 19, 2019, 3:44 p.m.