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hansenlab / minfi

Devel repository for minfi
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API for read.*() functions #116

Open PeteHaitch opened 7 years ago

PeteHaitch commented 7 years ago

Need to modify these to allow user to choose matrix or DelayedMatrix assays (and the DelayedMatrix backend)

# Current release
read.metharray(basenames, extended = FALSE, verbose = FALSE, force = FALSE)
# Current HDF5 branch (BACKEND arg has same semantics as used in DelayedArray)
read.metharray(basenames, extended = FALSE, verbose = FALSE, force = FALSE, 
               BACKEND = NULL)

# Proposal 1: Extend the BACKEND argument from definition used by DelayedArray
# If missing(BACKEND) then return matrix
# If BACKEND is supplied must be NULL (default in-memory backend, basically a 
# DelayedMatrix wrapper around a matrix seed) or one of 
# DelayedArray::supportedRealizationBackends()
read.metharray(basenames, extended = FALSE, verbose = FALSE, force = FALSE, 
               BACKEND)

# Proposal 2: In addition to BACKEND argument (with original semantics
# as used in DelayedArray), add a matrix/assaysAsMatrix/etc. argument 
read.metharray(basenames, extended = FALSE, verbose = FALSE, force = FALSE, 
               matrix = TRUE, BACKEND = NULL)
read.metharray(basenames, extended = FALSE, verbose = FALSE, force = FALSE, 
               assaysAsMatrix = TRUE, BACKEND = NULL)