readPgfEnv(file, readBody = TRUE, indices = NULL)
character(1)
providing a path to the PGF file to be
input.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.integer(n)
vector of positive integers
indicating which probesets to read. These integers must be
sorted (increasing) and unique.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 environment, but with appropriate default values.atomId
of atoms belonging to this probeset).probeId
of probes belonging to this atom). 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.