read.celfile.probeintensity.matrices: Read PM or MM from CEL file into matrices

Description Usage Arguments Value Author(s)

View source: R/read.probematrices.R

Description

This function reads PM, MM or both types of intensities into matrices. These matrices have all the probes for a probeset in adjacent rows

Usage

1
read.celfile.probeintensity.matrices(filenames, cdfInfo, rm.mask=FALSE, rm.outliers=FALSE, rm.extra=FALSE, verbose=FALSE, which= c("pm","mm","both"))

Arguments

filenames

a character vector of filenames

cdfInfo

a list with items giving PM and MM locations for desired probesets. In same structure as returned by make.cdf.package

rm.mask

a logical. Return these probes as NA if there are in the [MASK] section of the CEL file

rm.outliers

a logical. Return these probes as NA if there are in the [OUTLIERS] section of the CEL file

.

rm.extra

a logical. Return these probes as NA if there are in the [OUTLIERS] section of the CEL file

.

verbose

a logical. When true the parsing routine prints more information, typically useful for debugging.

which

a string specifing which probe type to return

Value

returns a list of matrix items. One matrix contains PM probe intensities, with probes in rows and arrays in columns

Author(s)

B. M. Bolstad <[email protected]>


affyio documentation built on May 6, 2019, 2:08 a.m.