Description Usage Arguments Value Author(s) Examples
The file provides the data to be converted to filevector format.
The file may provide the data only (no row and column names)
in which case col/row names may be left empty or provided in
separate files (in which case it is assumed that names are provided
only for the imported columns/rows – see skip-options).
There is an option to skip a number of
first ros and columns. The row and column names may also
be provided in the file itself, in which case one needs to
tell the row/column number providing column/row names.
Unless option "R_matrix" is set to TRUE, it is asumed that the
number of columns is always the same acorss the file. If above
option is provided, it is assumed that both column and row
names are provided in the file, and the first line contains
one column less than other lines (such is the case with
files produced from R using the function
write.table(...,col.names=TRUE,row.names=TRUE)
.
1 2 3 4 | text2databel(infile, outfile, colnames, rownames, skipcols, skiprows,
transpose = FALSE, R_matrix = FALSE, type = "DOUBLE",
cachesizeMb = 64, readonly = TRUE, naString = "NA",
unlinkTmpTransposeFiles = TRUE)
|
infile |
input text file name |
outfile |
output filevector file name; if missing, it is set to infile+".filevector" |
colnames |
where are the column names stored? If missing, no column names; if integer, this denotes the row of the input file where the column names are specified; if character string then the string specifies the name of the file with column names |
rownames |
where are the row names stored? If missing, no row names; if integer, this denotes the column of the input file where the row names are specified; if character string then the string specifies the name of the file with row names |
skipcols |
how many columns of the input file to skip |
skiprows |
how many rows of the input file to skip |
transpose |
whether the file is to be transposed |
R_matrix |
if true, the file format is assumed to follow
the format of R data matrix produced with
|
type |
data DatABEL type to use ("DOUBLE", "FLOAT", "INT", "UNSIGNED_INT", "UNSIGNED_SHORT_INT", "SHORT_INT", "CHAR", "UNSIGNED_CHAR") |
cachesizeMb |
cache size for the resulting 'databel-class' object |
readonly |
whether the resulting 'databel-class' object should be opened in readonly mode |
naString |
the string used for missing data (default: NA) |
unlinkTmpTransposeFiles |
Boolean to indicate whether the intermediate "_fvtmp.fvi/d" files should be deleted. Default: TRUE. These intermediate files are generated while transposing the filevector files. |
The converted file is stored in the file system, a databel-class object connection to the file is returned.
Yurii Aulchenko
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 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 | cat("this is an example which you can run if you can write to the
file system\n")
## Not run:
# create matrix
NC <- 5
NR <- 10
data <- matrix(rnorm(NC*NR),ncol=NC,nrow=NR)
rownames(data) <- paste("r",1:NR,sep="")
colnames(data) <- paste("c",1:NC,sep="")
data
# create text files
write.table(data, file="test_matrix_dimnames.dat", row.names=TRUE,
col.names=TRUE, quote=FALSE)
write.table(data, file="test_matrix_colnames.dat", row.names=FALSE,
col.names=TRUE, quote=FALSE)
write.table(data, file="test_matrix_rownames.dat", row.names=TRUE,
col.names=FALSE, quote=FALSE)
write.table(data, file="test_matrix_NOnames.dat", row.names=FALSE,
col.names=FALSE, quote=FALSE)
write(colnames(data), file="test_matrix.colnames")
write(rownames(data), file="test_matrix.rownames")
# generate identical data
text2databel(infile="test_matrix_dimnames.dat",
outfile="test_matrix_dimnames", R_matrix=TRUE)
x <- databel("test_matrix_dimnames")
data <- as(x, "matrix")
data
# convert text two filevector format
text2databel(infile="test_matrix_NOnames.dat",
outfile="test_matrix_NOnames.fvf",
colnames="test_matrix.colnames",
rownames="test_matrix.rownames")
x <- databel("test_matrix_NOnames.fvf")
if (!identical(data, as(x, "matrix"))) stop("not identical data")
text2databel(infile="test_matrix_NOnames.dat",
outfile="test_matrix_NOnames_T.fvf",
colnames="test_matrix.colnames",
rownames="test_matrix.rownames", transpose=TRUE)
x <- databel("test_matrix_NOnames_T.fvf")
if (!identical(data, t(as(x, "matrix")))) stop("not identical data")
text2databel(infile="test_matrix_rownames.dat",
outfile="test_matrix_rownames.fvf",
rownames=1, colnames="test_matrix.colnames")
x <- databel("test_matrix_rownames.fvf")
if (!identical(data, as(x, "matrix"))) stop("not identical data")
text2databel(infile="test_matrix_colnames.dat",
outfile="test_matrix_colnames.fvf",
colnames=1, rownames="test_matrix.rownames")
x <- databel("test_matrix_colnames.fvf")
if (!identical(data, as(x, "matrix"))) stop("not identical data")
text2databel(infile="test_matrix_dimnames.dat",
outfile="test_matrix_dimnames.fvf", R_matrix=TRUE)
x <- databel("test_matrix_dimnames.fvf")
if (!identical(data, as(x, "matrix"))) stop("not identical data")
# stupid extended matrix in non-R format
newmat <- matrix(-100, ncol=NC+3, nr=NR+2)
newmat[3:(NR+2), 4:(NC+3)] <- data
newmat[2, 4:(NC+3)] <- paste("c", 1:NC, sep="")
newmat[3:(NR+2), 3] <- paste("r", 1:NR, sep="")
newmat
write.table(newmat, file="test_matrix_strange.dat",
col.names=FALSE, row.names=FALSE, quote=FALSE)
text2databel(infile="test_matrix_strange.dat",
outfile="test_matrix_strange.fvf",
colnames=2, rownames=3)
x <- databel("test_matrix_strange.fvf")
if (!identical(data, as(x, "matrix"))) stop("not identical data")
## End(Not run)
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