Description Details Value See Also Examples
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.
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)
whatever is available.
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
cores
Number 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
σ^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
Shuffle
two bit mini hash table based on SSSE3
Shuffle256
two bit mini hash table based on AVX2
Packed
4-bit integer arithmetic based on SSE2
Packed256
4-bit integer arithmetic based on AVX2
Multiply
16-bit integer arithmetic based on SSE2
Multiply256
16-bit integer arithmetic based on AVX2
Twobit
two bit hash table
Threebit
three bit hash table
Hamming2
method used in PLINK
Hamming3
method used in PLINK
AutoCoding
method is chosen by the programme itself
NoSNPcoding
no coding, i.e. 32 bit integer
NoSNPcodingR
No coding: 32 bit integer, R code. Only for testing purposes.
NoSNPcodingAVX
No 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 σ^2 shall be also returned when the relationship matrix is calculated.
NULL
if any argument is given, and the full list of
arguments, otherwise.
1 | RFoptions()$genetics
|
Loading required package: RandomFieldsUtils
'miraculix' sees OMP, SSE2, but not AVX2, SSSE3.
Without appropriate SIMD instruction set, the calculations might be slow.
Consider recompiling 'miraculix' with flags e.g.,
install.packages("miraculix", configure.args="CXX_FLAGS=-march=native")
install.packages("miraculix", configure.args="CXX_FLAGS=-mavx2")
Alternatively consider installing 'miraculix'
from https://github.com/schlather/miraculix, i.e.,
install.packages("devtools")
library(devtools)
devtools::install_github("schlather/miraculix/pkg")
List of 6
$ any2bit : logi FALSE
$ centered : logi TRUE
$ digits : num 3
$ normalized : logi TRUE
$ returnsigma: logi FALSE
$ snpcoding : int 10
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