write.big.matrix | R Documentation |
Create a big.matrix
by reading from a
suitably-formatted ASCII file, or
write the contents of a big.matrix
to a file.
write.big.matrix(x, filename, row.names = FALSE, col.names = FALSE, sep = ",")
## S4 method for signature 'big.matrix,character'
write.big.matrix(x, filename, row.names = FALSE, col.names = FALSE, sep = ",")
read.big.matrix(
filename,
sep = ",",
header = FALSE,
col.names = NULL,
row.names = NULL,
has.row.names = FALSE,
ignore.row.names = FALSE,
type = NA,
skip = 0,
separated = FALSE,
backingfile = NULL,
backingpath = NULL,
descriptorfile = NULL,
binarydescriptor = FALSE,
extraCols = NULL,
shared = options()$bigmemory.default.shared
)
## S4 method for signature 'character'
read.big.matrix(
filename,
sep = ",",
header = FALSE,
col.names = NULL,
row.names = NULL,
has.row.names = FALSE,
ignore.row.names = FALSE,
type = NA,
skip = 0,
separated = FALSE,
backingfile = NULL,
backingpath = NULL,
descriptorfile = NULL,
binarydescriptor = FALSE,
extraCols = NULL,
shared = options()$bigmemory.default.shared
)
x |
a |
filename |
the name of an input/output file. |
row.names |
a vector of names, use them even if row names appear to exist in the file. |
col.names |
a vector of names, use them even if column names exist in the file. |
sep |
a field delimiter. |
header |
if |
has.row.names |
if |
ignore.row.names |
if |
type |
preferably specified, |
skip |
number of lines to skip at the head of the file. |
separated |
use separated column organization of the data instead of column-major organization. |
backingfile |
the root name for the file(s) for the cache of |
backingpath |
the path to the directory containing the file backing cache. |
descriptorfile |
the file to be used for the description of the filebacked matrix. |
binarydescriptor |
the flag to specify if the binary RDS format should
be used for the backingfile description, for subsequent use with
|
extraCols |
the optional number of extra columns to be appended to the matrix for future use. |
shared |
if |
Files must contain only one atomic type
(all integer
, for example). You, the user, should know whether
your file has row and/or column names, and various combinations of options
should be helpful in obtaining the desired behavior.
When reading from a file, if type
is not specified we try to
make a reasonable guess for you without
making any guarantees at this point.
Unless you have really large integer values, we recommend
you consider "short"
. If you have something that is essentially
categorical, you might even be able use "char"
, with huge memory
savings for large data sets.
Any non-numeric entry will be ignored and replaced with NA
,
so reading something that traditionally would be a data.frame
won't cause an error. A warning is issued.
Wishlist: we'd like to provide an option to ignore specified columns while doing reads. Or perhaps to specify columns targeted for factor or character conversion to numeric values. Would you use such features? Email us and let us know!
a big.matrix
object is returned by read.big.matrix
,
while write.big.matrix
creates an output file (a path could be part
of filename
).
John W. Emerson and Michael J. Kane bigmemoryauthors@gmail.com
big.matrix
# Without specifying the type, this big.matrix x will hold integers.
x <- as.big.matrix(matrix(1:10, 5, 2))
x[2,2] <- NA
x[,]
temp_dir = tempdir()
if (!dir.exists(temp_dir)) dir.create(temp_dir)
write.big.matrix(x, file.path(temp_dir, "foo.txt"))
# Just for fun, I'll read it back in as character (1-byte integers):
y <- read.big.matrix(file.path(temp_dir, "foo.txt"), type="char")
y[,]
# Other examples:
w <- as.big.matrix(matrix(1:10, 5, 2), type='double')
w[1,2] <- NA
w[2,2] <- -Inf
w[3,2] <- Inf
w[4,2] <- NaN
w[,]
write.big.matrix(w, file.path(temp_dir, "bar.txt"))
w <- read.big.matrix(file.path(temp_dir, "bar.txt"), type="double")
w[,]
w <- read.big.matrix(file.path(temp_dir, "bar.txt"), type="short")
w[,]
# Another example using row names (which we don't like).
x <- as.big.matrix(as.matrix(iris), type='double')
rownames(x) <- as.character(1:nrow(x))
head(x)
write.big.matrix(x, file.path(temp_dir, 'IrisData.txt'), col.names=TRUE,
row.names=TRUE)
y <- read.big.matrix(file.path(temp_dir, "IrisData.txt"), header=TRUE,
has.row.names=TRUE)
head(y)
# The following would fail with a dimension mismatch:
if (FALSE) y <- read.big.matrix(file.path(temp_dir, "IrisData.txt"),
header=TRUE)
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