readPgf {affxparser} | R Documentation |
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.
readPgf(file, indices = NULL)
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. |
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 i
th index of one vector (e.g.,
probesetId
) corresponds to the i
th 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. |
Martin Morgan mtmorgan@fhcrc.org
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.