Description Usage Arguments Details Value See Also Examples
Coerce to or create a compressed genomic matrix
1 2 3 4 5 6 | genomicmatrix(snps, individuals, file.type,
coding, header, IndividualsPerColumn,
DoubledIndividuals, leadingcolumns, loading,
...)
## S3 method for class 'genomicmatrix'
as(object, ...)
|
object, snps |
integer, matrix, vector, a haplomatrix or file name. See Details. |
individuals |
integer. See Details |
file.type |
if
|
coding |
if In case of 5 characters, a file with genomic data is assumed and the characters have the following meaning:
In case of 4 characters, a file with haplotype information is assumed and the characters have the following meaning:
The haplotype data is turned into genomic data. |
header |
integer. If
|
IndividualsPerColumn |
\ipc |
DoubledIndividuals |
\dindiv If |
leadingcolumns |
Integer. If |
loading |
logical. If |
... |
options, see |
genomicmatrix
creates a
compressed matrix according to the coding scheme given by
RFoptions()$genetics$snpcoding
.
In case snps
is a string, i.e., a file name, the extension of
the file name predefines the file.type
:
=‘beagle’
=‘beagle’
=‘plink’
=‘plink2’
=‘plink2’
=‘plinkbinary’
The definition can be overwritten by file.type
. The latter
can be overwritten by all other options (except individuals
).
If individuals
is given, genomicmatrix
creates a
snps
\times individuals
compressed data matrix filled
with zeros. The matrix can be modified afterwards by
fillGeno
.
If a haplomatrix is given, it is
transformed into a genomicmatrix
.
If genomicmatrix
is given, the matrix is returned as is and a
warning is given.
Both functions, genomicmatrix
and as
have exactly
the same behavior execept for loading
which is TRUE
for
genomicmatrix
by default and fixed to be FALSE
for as.genomicmatrix
.
an object of class genomatrix
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
set.seed(0)
snps <- 100
indiv <- 10
M <- matrix(sample(0:2, snps * indiv, replace=TRUE), nrow = snps)
(GM <- genomicmatrix(M))
stopifnot(all(as.matrix(GM) == M))
## There is a difference between genomicmatrix and as.genomicmatrix
## in case of files: 'as.genomicmatrix' creates only a pointer to
## the file, while 'genomicmatrix' reads the file
file <- "miraculix"
if (interactive() && !file.exists(paste0(file, ".bgl"))) {
f <- rhaplo(indiv=100, loci=1000, file=file, file.type="beagle")
print(f)
print(G <- as.genomicmatrix(f))
print(g <- genomicmatrix(f))
Print(object.size(G), object.size(g)) ## g needs much more memory
file.remove(f)
}
|
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