RFoptions sets and returns control arguments for
diverse packages (miraculix, RandomFields).
RFoptions should not be used within parallelizing R
commands such as mclapply in package parallel.
NULL if any argument is given, and the full list of
arguments, otherwise.
The specific parameters for miraculix are the following.
See RFoptions in
RandomFieldsUtils
for further options.
logical.
If TRUE then always the most time efficient code
is used among
TwoBit (no SIMD needed)
Packed (SSE2 needed)
Shuffle (SSSE3 needed)
Shuffle256 (AVX2 needed)
Default : FALSE. This value might change to TRUE in
future.
logical or numerical.
If TRUE the \(P\) matrix is substracted before the
crossproduct of the the SNP matrix is calculated,
see relationshipMatrix for the \(P\) matrix.
If numeric, then the length of this vector must equal the number
of SNPs per individual. Then this vector is substracted for each
individual.
Furthermore, normalized is FALSE.
As the size of centered can be large, this vector is never
returned by RFoption(); instead NA is returned.
Note that centered also sets the value of normalized.
Default : TRUE
coresNumber of cores for multicore algorithms.
OBSOLETE. scalar.
If digits is negative no rounding is performed.
Else the matrix \(P\) when calculating the relationsship matrix
\((M-P)^T(M-P)\) is rounded to the given number of absolute (not
significant) digits.
Default : 3.0.
logical.
If TRUE the relationship matrix is normalized by
\(\sigma^2\), see relationshipMatrix.
Its value is set to the value of centered whenever
the value of centered is changed. So normalized
must be set always after centered,
e.g. RFoptions(centered=TRUE, normalized=FALSE), but not
RFoptions(normalized=FALSE, centered=TRUE).
Default : TRUE
integer. Possible values are
Shuffletwo bit mini hash table based on SSSE3
Shuffle256two bit mini hash table based on AVX2
Packed4-bit integer arithmetic based on SSE2
Packed2564-bit integer arithmetic based on AVX2
Multiply16-bit integer arithmetic based on SSE2
Multiply25616-bit integer arithmetic based on AVX2
Twobittwo bit hash table
Threebitthree bit hash table
Hamming2method used in PLINK
Hamming3method used in PLINK
AutoCodingmethod is chosen by the programme itself
NoSNPcodingno coding, i.e. 32 bit integer
NoSNPcodingRNo coding: 32 bit integer, R code. Only for testing purposes.
NoSNPcodingAVXNo coding: AVX implementation if available (double precision or integer).
In for loops that run through all available methods
the constants FirstGenuineMethod and
LastGenuineMethod
might be useful.
In case of the package MoPBS or if interest is in the 2 bit methods
only, use the constants FirstMoBPSmethod and
LastMoBPSmethod.
In case the names of the method is needed, use
SNPCODING_NAMES[snp_coding + 1].
Default : Shuffle
logical. Whether \(\sigma^2\) shall be also returned when the relationship matrix is calculated.
# NOT RUN {
<!-- % library(adoption) -->
# }
# NOT RUN {
RFoptions()$genetics
# }
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