readPgf: Parsing a PGF file using Affymetrix Fusion SDK

Description Usage Arguments Value Author(s) See Also

View source: R/readPgf.R

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

1
readPgf(file, indices = NULL)

Arguments

file

character(1) providing a path to the PGF file to be input.

indices

integer(n) a vector of indices of the probesets to be read.

Value

An list. 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 list, 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.


affxparser documentation built on Nov. 1, 2018, 2:25 a.m.