Description Usage Arguments Details Value Author(s) See Also Examples
Create a new or open existing filematrix
object.
fm.create
creates a new filematrix.
If a filematrix with this name exists, it is overwritten (destroyed).
fm.create.from.matrix
creates a new filematrix copy of
an existing R matrix.
fm.open
opens an existing filematrix for read/write access.
fm.load
loads entire existing filematrix
into memory as an ordinary R matrix.
fm.create.from.text.file
reads a matrix from a text file
into a new filematrix.
The rows in the text file become columns in the filematrix.
The transposition happens because the text files stores data by rows and
filematrices store data by columns.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | fm.create(
filenamebase,
nrow = 0,
ncol = 1,
type = "double",
size = NULL,
lockfile = NULL)
fm.create.from.matrix(
filenamebase,
mat,
size = NULL,
lockfile = NULL)
fm.open(
filenamebase,
readonly = FALSE,
lockfile = NULL)
fm.load(filenamebase, lockfile = NULL)
fm.create.from.text.file(
textfilename,
filenamebase,
skipRows = 1,
skipColumns = 1,
sliceSize = 1000,
omitCharacters = "NA",
delimiter = "\t",
rowNamesColumn = 1,
type = "double",
size = NULL)
## S4 method for signature 'filematrix'
close(con)
closeAndDeleteFiles(con)
|
filenamebase |
Name without extension for the files storing the filematrix. |
nrow |
Number of rows in the matrix. Values over 2^32 are supported. |
ncol |
Number of columns in the matrix. Values over 2^32 are supported. |
type |
The type of values stored in the matrix.
Can be either |
size |
Size of each item of the matrix in bytes. |
mat |
Regular R matrix, to be copied into a new filematrix. |
readonly |
If |
textfilename |
Name of the text file with matrix data, to be copied into a new filematrix. |
skipRows |
Number of rows with column names.
The matrix values are expected after first |
skipColumns |
Number of columns before matrix values begin. Can be zero. |
sliceSize |
The text file with matrix is read in chuncks of |
omitCharacters |
The text string representing missing values.
Default value is |
delimiter |
The delimiter separating values in the text matrix file. |
rowNamesColumn |
The row names are taken from the |
con |
A filematrix object. |
lockfile |
Optional. Name of a lock file (file is overwritten). Used to avoid simultaneous operations by multiple R instances accessing the same filematrix or different filematrices on the same hard drive. Do not use if not sure. |
Once created or opened, a filematrix object can be accessed
as an ordinary matrix using both matrix fm[,]
and
vector fm[]
indexing.
The indices can be integer (no zeros) or logical vectors.
Returns a filematrix
object.
The object can be closed with close
command or
closed and deleted from disk with closeAndDeleteFiles
command.
Andrey A Shabalin andrey.shabalin@gmail.com
For more on the use of filematrices see filematrix
.
Run browseVignettes("filematrix")
for the list of vignettes.
1 2 3 4 5 6 7 8 9 10 11 | # Create a 10x10 matrix
fm = fm.create(filenamebase=tempfile(), nrow=10, ncol=10)
# Change values in the top 3x3 corner
fm[1:3,1:3] = 1:9
# View the values in the top 4x4 corner
fm[1:4,1:4]
# Close and delete the filematrix
closeAndDeleteFiles(fm)
|
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