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affxparser (version 1.44.0)

readPgfEnv: Parsing a PGF file using Affymetrix Fusion SDK

Description

This function parses a PGF file using the Affymetrix Fusion SDK. PGF (probe group) files describe probes present within probe sets, including the type (e.g., pm, mm) of the probe and probeset.

Usage

readPgfEnv(file, readBody = TRUE, indices = NULL)

Arguments

file
character(1) providing a path to the PGF file to be input.
readBody
logical(1) indicating whether the entire file should be parsed (TRUE) or only the file header information describing the chips to which the file is releavant.
indices
integer(n) vector of positive integers indicating which probesets to read. These integers must be sorted (increasing) and unique.

Value

An environment. The header element is always present; the remainder are present when readBody=TRUE.The elements present when readBody=TRUE describe probe sets, atoms, and probes. Elements within probe sets, for instance, are coordinated such that the ith index of one vector (e.g., probesetId) corresponds to the ith index of a second vector (e.g., probesetType). The atoms contained within probeset i are in positions probesetStartAtom[i]:(probesetStartAtom[i+1]-1) of the atom vectors. A similar map applies to probes within atoms, using atomStartProbe as the index.The PGF file format includes optional elements; these elements are always present in the environment, but with appropriate default values.
header
A list with information about the PGF file. The list contains elements described in the PGF file format document referenced below.
probesetId
integer vector of probeset identifiers.
probesetType
character vector of probeset types. Types are described in the PGF file format document.
probesetName
character vector of probeset names.
probesetStartAtom
integer vector of the start index (e.g., in the element atomId of atoms belonging to this probeset).
atomId
integer vector of atom identifiers.
atomExonPosition
integer vector of probe interrogation position relative to the target sequence.
atomStartProbe
integer vector of the start index (e.g., in the element probeId of probes belonging to this atom).
probeId
integer vector of probe identifiers.
probeType
character vector of probe types. Types are described in the PGF file format document.
probeGcCount
integer vector of probe GC content.
probeLength
integer vector of probe lengths.
probeInterrogationPosition
integer vector of the position, within the probe, at which interrogation occurs.
probeSequence
character vector of the probe sequence.

See Also

https://www.affymetrix.com/support/developer/fusion/File_Format_PGF_aptv161.pdf describes PGF file content.

The internal function .pgfProbeIndexFromProbesetIndex provides a map between the indicies of probe set entries and the indicies of the probes contained in the probe set.