readPgfEnv: Parsing a PGF file using Affymetrix Fusion SDK

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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 relevant.
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.

Author(s)

Martin Morgan

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 indices of probe set entries and the indices of the probes contained in the probe set.

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.