as.genomic: Transform a Matrix to a Compressed Matrix
In miraculix: Algebraic and Statistical Functions for Genetics

Description Usage Arguments Details Value See Also Examples

Coerce to or create a compressed genomic matrix

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 `object` is a filename then the precise coding of preceding headers, preceding columns, and the coding of the data can be very different. Instead of giving all the arguments `coding`, ..., `leadingcolumns`, the `file.type` can be given: ‘beagle’ i.e.`coding="AB? "` ‘plink’ i.e. `coding="AB? "` ‘plink2’ i.e. `coding="12? ",` ‘plinkbinary’ i.e. `coding="12345"`
`coding`	if `object` is a filename then `coding` is a string of 4 or 5 characters. In case of 5 characters, a file with genomic data is assumed and the characters have the following meaning: 1st code for 0 2nd code for 1 3rd code for 2 4th code for NA 5th the field separator character In case of 4 characters, a file with haplotype information is assumed and the characters have the following meaning: 1st code for 0 2nd code for 1 3rd code for NA 4th the field separator character The haplotype data is turned into genomic data.
`header`	integer. If `object` is a filename then `header` has the following meaning positive `header`: `header` gives the number of preceding lines in the file that will be ignored. An ASCII file is assumed in this case. negative `header`: a binary file is assumed and -`header` gives the number of preceding characters that will be jumped.
`IndividualsPerColumn`	\ipc
`DoubledIndividuals`	\dindiv If `object` is a filename, coding has 4 characters (i.e. it is a haplo file)
`leadingcolumns`	Integer. If `object` is a filename then `leadingcolumns` gives the number of first columns in the file that are ignored.
`loading`	logical. If `object` is a filename then `loading` decides whether the file contents is read into RAM. Otherwise the file is read on the fly whenever possible. `loading` is `TRUE` for `genomicmatrix` and `FALSE` otherwise.
`...`	options, see `RFoptions`

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:

‘.txt’: =‘beagle’
‘.bgl’: =‘beagle’
‘.phased’: =‘plink’
‘.tped’: =‘plink2’
‘.ped’: =‘plink2’
‘.bed’: =‘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

haplomatrix as.matrix

 
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)
}