readCdfCellIndices: Reads (one-based) cell indices of units (probesets) in an...

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

Reads (one-based) cell indices of units (probesets) in an Affymetrix CDF file

Description

Reads (one-based) cell indices of units (probesets) in an Affymetrix CDF file.

Usage

readCdfCellIndices(filename, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"),
  verbose=0)

Arguments

filename	The filename of the CDF file.
units	An integer vector of unit indices specifying which units to be read. If NULL, all units are read.
stratifyBy	A character string specifying which and how elements in group fields are returned. If "nothing", elements are returned as is, i.e. as vectors. If "pm"/"mm", only elements corresponding to perfect-match (PM) / mismatch (MM) probes are returned (as vectors). If "pmmm", elements are returned as a matrix where the first row holds elements corresponding to PM probes and the second corresponding to MM probes. Note that in this case, it is assumed that there are equal number of PMs and MMs; if not, an error is generated. Moreover, the PMs and MMs may not even be paired, i.e. there is no guarantee that the two elements in a column corresponds to a PM-MM pair.
verbose	An integer specifying the verbose level. If 0, the file is parsed quietly. The higher numbers, the more details.

Value

A named list where the names corresponds to the names of the units read. Each unit element of the list is in turn a list structure with one element groups which in turn is a list. Each group element in groups is a list with a single field named indices. Thus, the structure is

    cdf
     +- unit #1
     |   +- "groups"
     |       +- group #1
     |       |   +- "indices"
     |       |  group #2
     |       |   +- "indices"
     |       .
     |       +- group #K
     |           +- "indices"
     +- unit #2
     .
     +- unit #J
  

This is structure is compatible with what readCdfUnits() returns.

Note that these indices are one-based.

Cell indices are one-based

Note that in affxparser all cell indices are by convention one-based, which is more convenient to work with in R. For more details on one-based indices, see 2. Cell coordinates and cell indices.

Author(s)

Henrik Bengtsson

See Also

readCdfUnits().

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