[Genabel-commits] r1799 - pkg/DatABEL/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Aug 12 11:54:42 CEST 2014
Author: lckarssen
Date: 2014-08-12 11:54:42 +0200 (Tue, 12 Aug 2014)
New Revision: 1799
Added:
pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd
Modified:
pkg/DatABEL/man/DatABEL-package.Rd
pkg/DatABEL/man/apply2dfo.Rd
pkg/DatABEL/man/databel-class.Rd
pkg/DatABEL/man/databel.Rd
pkg/DatABEL/man/databel2matrix.Rd
pkg/DatABEL/man/databel2text.Rd
pkg/DatABEL/man/extract_text_file_columns.Rd
pkg/DatABEL/man/get_temporary_file_name.Rd
pkg/DatABEL/man/make_empty_fvf.Rd
pkg/DatABEL/man/matrix2databel.Rd
pkg/DatABEL/man/process_lm_output.Rd
pkg/DatABEL/man/text2databel.Rd
Log:
DatABEL documentation now generated from the roxygen2 documentation (by devtools::document())
Modified: pkg/DatABEL/man/DatABEL-package.Rd
===================================================================
--- pkg/DatABEL/man/DatABEL-package.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/DatABEL-package.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\docType{package}
\name{DatABEL-package}
\alias{"DatABEL"}
@@ -5,20 +6,23 @@
\title{DatABEL package for fast consecutive access to large out-of-RAM
stored matrices}
\description{
-A package interfacing FILEVECTOR C++ library for storage of
-and fast consecutive access to large data matrices in
-out-of-RAM disk mode with regulated cache size. Columns of
-matrix are accessible very quickly.
+A package interfacing FILEVECTOR C++ library
+for storage of and fast consecutive access to
+large data matrices in out-of-RAM disk mode
+with regulated cache size. Columns of matrix
+are accessible very quickly.
}
\author{
Yurii Aulchenko (R code), Stepan Yakovenko (R and C++
code), Andrey Chernyh (C++ code)
}
\seealso{
-\code{\link{apply2dfo}}, \code{\link{databel2matrix}},
+\code{\link{apply2dfo}},
+\code{\link{databel2matrix}},
\code{\link{databel2text}},
\code{\link{extract_text_file_columns}},
-\code{\link{matrix2databel}}, \code{\link{text2databel}},
+\code{\link{matrix2databel}},
+\code{\link{text2databel}},
\code{\linkS4class{databel}}
}
Modified: pkg/DatABEL/man/apply2dfo.Rd
===================================================================
--- pkg/DatABEL/man/apply2dfo.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/apply2dfo.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{apply2dfo}
\alias{apply2dfo}
\title{applies a function to a 'databel' object}
@@ -6,41 +7,40 @@
outclass = "matrix", outfile, type = "DOUBLE", transpose = TRUE)
}
\arguments{
- \item{dfodata}{'databel' object which is iterated over}
+\item{dfodata}{'databel' object which is iterated over}
- \item{anFUN}{user-defined analysis function}
+\item{anFUN}{user-defined analysis function}
- \item{MAR}{which margin to iterate over (default = 2,
- usually these are 'columns' used to store SNP data)}
+\item{MAR}{which margin to iterate over (default = 2, usually
+these are 'columns' used to store SNP data)}
- \item{procFUN}{function to process the output and present
- that as a fixed-number-of-columns matrix or fixed-length
- vector. Can be missing if standard functions listed below
- are used. Pre-defined processors included are
- "process_lm_output" (can process functions "lm", "glm",
- "coxph") and "process_simple_output" (process output from
- "sum", "prod", "sum_not_NA" [no. non-missing obs],
- "sum_NA" [no. missing obs.])}
+\item{procFUN}{function to process the output and present that as a
+fixed-number-of-columns matrix or fixed-length vector. Can be
+missing if standard functions listed below are used. Pre-defined
+processors included are "process_lm_output" (can process functions
+"lm", "glm", "coxph") and "process_simple_output" (process output
+from "sum", "prod", "sum_not_NA" [no. non-missing obs], "sum_NA"
+[no. missing obs.])}
- \item{outclass}{output to ("matrix" or "databel")}
+\item{outclass}{output to ("matrix" or "databel")}
- \item{outfile}{if output class is "databel", the
- generated object is bound to the \code{outfile}}
+\item{outfile}{if output class is "databel", the generated object
+is bound to the \code{outfile}}
- \item{type}{if output class is "databel", what data type
- to use for storage}
+\item{type}{if output class is "databel", what data type to use for
+storage}
- \item{transpose}{whether to transpose the output}
+\item{transpose}{whether to transpose the output}
- \item{...}{arguments passed to the \code{anFUN}}
+\item{...}{arguments passed to the \code{anFUN}}
}
\value{
A matrix (or 'databel'-matrix) containing results of
applying the function
}
\description{
-An iterator applying a user-defined function to an object
-of 'databel-class'.
+An iterator applying a user-defined function to
+an object of 'databel-class'.
}
\examples{
a <- matrix(rnorm(50), 10, 5)
Added: pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd
===================================================================
--- pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd (rev 0)
+++ pkg/DatABEL/man/checkPackageVersionOnCRAN.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -0,0 +1,33 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
+\name{checkPackageVersionOnCRAN}
+\alias{checkPackageVersionOnCRAN}
+\title{checks what is the version of package on CRAN}
+\usage{
+checkPackageVersionOnCRAN(packageName)
+}
+\arguments{
+\item{packageName}{name of the package to check}
+}
+\value{
+string containing CRAN version
+of the package
+}
+\description{
+Checks what is the version of package on CRAN.
+The CRAN page (baseUrlCRAN+packageName) is checked
+and parsed extracting the line with
+"Package source: packageName_Version.tar.gz"
+e.g.
+"Package source: GenABEL_1.6-9.tar.gz"
+and then the 'Version' is returned.
+Otherwise, NULL is returned.
+}
+\examples{
+library(GenABEL)
+packageVersion("GenABEL")
+checkPackageVersionOnCRAN("GenABEL")
+}
+\author{
+Yurii Aulchenko
+}
+
Modified: pkg/DatABEL/man/databel-class.Rd
===================================================================
--- pkg/DatABEL/man/databel-class.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/databel-class.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,22 +1,140 @@
-\docType{methods}
-\name{databel}
-\alias{databel}
+% Generated by roxygen2 (4.0.1): do not edit by hand
+\docType{class}
+\name{databel-class}
+\alias{[,databel-method}
+\alias{[<-,databel-method}
+\alias{backingfilename}
+\alias{backingfilename,databel-method}
+\alias{cachesizeMb}
+\alias{cachesizeMb,databel-method}
+\alias{cachesizeMb<-}
+\alias{cachesizeMb<-,databel-method}
+\alias{connect}
+\alias{connect,databel-method}
\alias{databel-class}
+\alias{dim,databel-method}
+\alias{dimnames,databel-method}
+\alias{dimnames<-,databel-method}
+\alias{disconnect}
+\alias{disconnect,databel-method}
+\alias{get_dimnames}
+\alias{get_dimnames,databel-method}
+\alias{length,databel-method}
+\alias{save_as}
+\alias{save_as,databel-method}
+\alias{setReadOnly<-}
+\alias{setReadOnly<-,databel-method}
+\alias{set_dimnames<-}
+\alias{set_dimnames<-,databel-method}
+\alias{show,databel-method}
\title{DatABEL class}
+\usage{
+\S4method{show}{databel}(object)
+
+\S4method{dim}{databel}(x)
+
+\S4method{length}{databel}(x)
+
+\S4method{dimnames}{databel}(x)
+
+\S4method{dimnames}{databel}(x) <- value
+
+\S4method{[}{databel}(x, i, j, drop)
+
+\S4method{[}{databel}(x, i, j) <- value
+
+get_dimnames(object)
+
+set_dimnames(x) <- value
+
+backingfilename(object)
+
+cachesizeMb(object)
+
+cachesizeMb(x) <- value
+
+save_as(x, rows, cols, file, cachesizeMb = 64, readonly = TRUE)
+
+connect(object, readonly = TRUE)
+
+disconnect(object)
+
+setReadOnly(x) <- value
+}
+\arguments{
+\item{j}{Column index}
+
+\item{file}{Filename to save to}
+
+\item{rows}{Index for the rows}
+
+\item{cols}{Index for the columns}
+
+\item{cachesizeMb}{Amount (in MB) of RAM to use for caching DatABEL
+data.}
+
+\item{readonly}{Boolean that specifies whether the file is to be
+used in read-only mode or not}
+
+\item{object}{Any R object}
+
+\item{x}{an \R object, for example a matrix, array or data frame.}
+
+\item{value}{For the default method, either \code{NULL} or
+ a numeric vector, which is coerced to integer (by truncation).}
+
+\item{i}{
+ indices specifying elements to extract or replace. Indices are
+ \code{numeric} or \code{character} vectors or empty (missing) or
+ \code{NULL}. Numeric values are coerced to integer as by
+ \code{\link{as.integer}} (and hence truncated towards zero).
+ Character vectors will be matched to the \code{\link{names}} of the
+ object (or for matrices/arrays, the \code{\link{dimnames}}):
+ see \sQuote{Character indices} below for further details.
+
+ For \code{[}-indexing only: \code{i}, \code{j}, \code{\dots} can be
+ logical vectors, indicating elements/slices to select. Such vectors
+ are recycled if necessary to match the corresponding extent.
+ \code{i}, \code{j}, \code{\dots} can also be negative integers,
+ indicating elements/slices to leave out of the selection.
+
+ When indexing arrays by \code{[} a single argument \code{i} can be a
+ matrix with as many columns as there are dimensions of \code{x}; the
+ result is then a vector with elements corresponding to the sets of
+ indices in each row of \code{i}.
+
+ An index value of \code{NULL} is treated as if it were \code{integer(0)}.
+ }
+
+\item{drop}{For matrices and arrays. If \code{TRUE} the result is
+ coerced to the lowest possible dimension (see the examples). This
+ only works for extracting elements, not for the replacement. See
+ \code{\link{drop}} for further details.
+ }
+}
\description{
-DatABEL class
+DatABEL stores matrix-shape data in such a way that it can be
+retrieved fast.
}
+\section{Slots}{
+
+\describe{
+\item{\code{usedRowIndex}}{(\code{"integer"})}
+
+\item{\code{usedColIndex}}{(\code{"integer"})}
+
+\item{\code{uninames}}{(\code{"list"})}
+
+\item{\code{backingfilename}}{Name of the (stem of the) file that contains
+the data stored in DatABEL format ()\code{"character"})}
+
+\item{\code{cachesizeMb}}{(\code{"integer"})}
+
+\item{\code{data}}{(\code{"externalptr"})}
+}}
\note{
Will extend description here
}
-\section{Slots}{
- \describe{ \item{\code{usedRowIndex}:}{\code{"integer"}}
- \item{\code{usedColIndex}:}{\code{"integer"}}
- \item{\code{uninames}:}{\code{"list"}}
- \item{\code{backingfilename}:}{\code{"character"}}
- \item{\code{cachesizeMb}:}{\code{"integer"}}
- \item{\code{data}:}{\code{"externalptr"}} }
-}
\author{
Yurii Aulchenko
}
Modified: pkg/DatABEL/man/databel.Rd
===================================================================
--- pkg/DatABEL/man/databel.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/databel.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{databel}
\alias{databel}
\title{initiates databel object}
@@ -5,16 +6,15 @@
databel(baseobject, cachesizeMb = 64, readonly = TRUE)
}
\arguments{
- \item{baseobject}{name of the file or
- \link{databel-class} object}
+\item{baseobject}{name of the file or \link{databel-class} object}
- \item{cachesizeMb}{cache size (amount of RAM) to be used}
+\item{cachesizeMb}{cache size (amount of RAM) to be used}
- \item{readonly}{readonly flag}
+\item{readonly}{readonly flag}
}
\description{
-this is a simple wrapper for the "new" function creating a
-databel object
+this is a simple wrapper for the "new" function
+creating a databel object
}
\author{
Yurii Aulchenko
Modified: pkg/DatABEL/man/databel2matrix.Rd
===================================================================
--- pkg/DatABEL/man/databel2matrix.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/databel2matrix.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{databel2matrix}
\alias{databel2matrix}
\title{converts 'databel' to matrix}
@@ -5,20 +6,19 @@
databel2matrix(from, rows, cols)
}
\arguments{
- \item{from}{'databel' matrix}
+\item{from}{'databel' matrix}
- \item{rows}{which rows to include}
+\item{rows}{which rows to include}
- \item{cols}{which columns to include}
+\item{cols}{which columns to include}
}
\value{
object of \code{\linkS4class{matrix}} class
}
\description{
-Converts a \code{\linkS4class{databel}} object to a regular
-R matrix. This is the procedure used by the "as" converting
-to DatABEL objects, in which case a temporary file name is
-created.
+Converts a \code{\linkS4class{databel}} object to a regular R matrix.
+This is the procedure used by the "as" converting to DatABEL objects,
+in which case a temporary file name is created.
}
\author{
Stepan Yakovenko
Modified: pkg/DatABEL/man/databel2text.Rd
===================================================================
--- pkg/DatABEL/man/databel2text.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/databel2text.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{databel2text}
\alias{databel2text}
\title{Exports DatABEL object to a text file}
@@ -6,17 +7,17 @@
col.names = TRUE, transpose = FALSE)
}
\arguments{
- \item{databel}{DatABEL object}
+\item{databel}{DatABEL object}
- \item{file}{output file name}
+\item{file}{output file name}
- \item{NAString}{string to replace NA with}
+\item{NAString}{string to replace NA with}
- \item{row.names}{export row names if TRUE}
+\item{row.names}{export row names if TRUE}
- \item{col.names}{export col names if TRUE}
+\item{col.names}{export col names if TRUE}
- \item{transpose}{whether the matrix should be transposed}
+\item{transpose}{whether the matrix should be transposed}
}
\description{
Exports DatABEL object to a text file
Modified: pkg/DatABEL/man/extract_text_file_columns.Rd
===================================================================
--- pkg/DatABEL/man/extract_text_file_columns.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/extract_text_file_columns.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{extract_text_file_columns}
\alias{extract_text_file_columns}
\title{extracts columns from text file}
@@ -5,16 +6,16 @@
extract_text_file_columns(file, whichcols)
}
\arguments{
- \item{file}{file name}
+\item{file}{file name}
- \item{whichcols}{which columns to extract}
+\item{whichcols}{which columns to extract}
}
\value{
matrix of strings with values from that columns
}
\description{
-Extracts a column from text file to a matrix. If in a
-particular file line the number of columns is less then a
-column specified, returns last column!
+Extracts a column from text file to a matrix.
+If in a particular file line the number of columns is less
+then a column specified, returns last column!
}
Modified: pkg/DatABEL/man/get_temporary_file_name.Rd
===================================================================
--- pkg/DatABEL/man/get_temporary_file_name.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/get_temporary_file_name.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{get_temporary_file_name}
\alias{get_temporary_file_name}
\title{generates temporary file name}
@@ -5,11 +6,11 @@
get_temporary_file_name(path = ".", withFVext = TRUE)
}
\arguments{
- \item{path}{path to directory where the temporary file
- will be located}
+\item{path}{path to directory where the temporary file will be
+located}
- \item{withFVext}{whether function should check presence
- of *FVD and *FVI files too}
+\item{withFVext}{whether function should check presence of *FVD and
+*FVI files too}
}
\description{
function to generate temporary file name
Modified: pkg/DatABEL/man/make_empty_fvf.Rd
===================================================================
--- pkg/DatABEL/man/make_empty_fvf.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/make_empty_fvf.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{make_empty_fvf}
\alias{make_empty_fvf}
\title{makes empty filevector object}
@@ -6,28 +7,23 @@
cachesizeMb = 64, readonly = FALSE)
}
\arguments{
- \item{name}{name fo the file to be assoiated with new
- object}
+\item{name}{name fo the file to be assoiated with new object}
- \item{nvariables}{number of variables (R columns)}
+\item{nvariables}{number of variables (R columns)}
- \item{nobservations}{number of observations (R rows)}
+\item{nobservations}{number of observations (R rows)}
- \item{type}{data type of the object
- ("UNSIGNED_SHORT_INT", "SHORT_INT", "UNSIGNED_INT",
- "INT", "FLOAT", "DOUBLE", "CHAR", "UNSIGNED_CHAR")}
+\item{type}{data type of the object ("UNSIGNED_SHORT_INT",
+"SHORT_INT", "UNSIGNED_INT", "INT", "FLOAT", "DOUBLE", "CHAR", "UNSIGNED_CHAR")}
- \item{cachesizeMb}{what cache size to use for newly
- generated 'databel' object}
+\item{cachesizeMb}{what cache size to use for newly generated 'databel' object}
- \item{readonly}{whether to open new 'databel' in readonly
- mode}
+\item{readonly}{whether to open new 'databel' in readonly mode}
}
\value{
databel object; also file is created in file system
}
\description{
-function to generate empty filevector object (and disk
-files)
+function to generate empty filevector object (and disk files)
}
Modified: pkg/DatABEL/man/matrix2databel.Rd
===================================================================
--- pkg/DatABEL/man/matrix2databel.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/matrix2databel.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{matrix2databel}
\alias{matrix2databel}
\title{converts matrix to 'databel'}
@@ -6,28 +7,24 @@
readonly = FALSE)
}
\arguments{
- \item{from}{R matrix}
+\item{from}{R matrix}
- \item{filename}{which FILEVECTOR BASE file name to use}
+\item{filename}{which FILEVECTOR BASE file name to use}
- \item{cachesizeMb}{cache size to be used when accessing
- the object}
+\item{cachesizeMb}{cache size to be used when accessing the object}
- \item{type}{type of data to use for storage ("DOUBLE",
- "FLOAT", "INT", "UNSIGNED_INT", "UNSIGNED_SHORT_INT",
- "SHORT_INT", "CHAR", "UNSIGNED_CHAR")}
+\item{type}{type of data to use for storage ("DOUBLE", "FLOAT", "INT",
+"UNSIGNED_INT", "UNSIGNED_SHORT_INT", "SHORT_INT", "CHAR", "UNSIGNED_CHAR")}
- \item{readonly}{whether to generate new 'databel' in read
- only mode}
+\item{readonly}{whether to generate new 'databel' in read only mode}
}
\value{
object of class \code{\linkS4class{databel}}
}
\description{
-Converts regular R matrix to \code{\linkS4class{databel}}
-object. This is the procedure used by "as" converting to
-DatABEL objects, in which case a temporary file name is
-created
+Converts regular R matrix to \code{\linkS4class{databel}} object.
+This is the procedure used by "as" converting to DatABEL objects,
+in which case a temporary file name is created
}
\author{
Yurii Aulchenko
Modified: pkg/DatABEL/man/process_lm_output.Rd
===================================================================
--- pkg/DatABEL/man/process_lm_output.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/process_lm_output.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{process_lm_output}
\alias{process_lm_output}
\alias{process_simple_output}
@@ -5,22 +6,20 @@
\alias{sum_not_NA}
\title{'apply2dfo'-associated functions}
\usage{
-process_lm_output(lmo,verbosity=2)
+process_lm_output(lmo, verbosity=2)
}
\arguments{
- \item{lmo}{object returned by analysis with "lm", "glm",
- etc.}
+\item{lmo}{object returned by analysis with "lm", "glm", etc.}
- \item{verbosity}{verbosity}
+\item{verbosity}{verbosity}
}
\description{
A number of functions used in conjunction with 'apply2dfo'.
-Standardly supported apply2dfo's anFUN analysis functions
-include 'lm', 'glm', 'coxph', 'sum', 'prod', "sum_not_NA"
-(no. non-missing obs), and "sum_NA" (no. missing obs.).
-Pre-defined processing functions include
-"process_lm_output" (can process functions "lm", "glm",
-"coxph") and "process_simple_output" (process output from
+Standardly supported apply2dfo's anFUN analysis functions include
+'lm', 'glm', 'coxph', 'sum', 'prod', "sum_not_NA" (no. non-missing
+obs), and "sum_NA" (no. missing obs.). Pre-defined processing
+functions include "process_lm_output" (can process functions "lm",
+"glm", "coxph") and "process_simple_output" (process output from
"sum", "prod", "sum_not_NA", "sum_NA")
}
\examples{
Modified: pkg/DatABEL/man/text2databel.Rd
===================================================================
--- pkg/DatABEL/man/text2databel.Rd 2014-08-12 09:53:30 UTC (rev 1798)
+++ pkg/DatABEL/man/text2databel.Rd 2014-08-12 09:54:42 UTC (rev 1799)
@@ -1,3 +1,4 @@
+% Generated by roxygen2 (4.0.1): do not edit by hand
\name{text2databel}
\alias{text2databel}
\title{converts text file to filevector format}
@@ -8,73 +9,68 @@
unlinkTmpTransposeFiles = TRUE)
}
\arguments{
- \item{infile}{input text file name}
+\item{infile}{input text file name}
- \item{outfile}{output filevector file name; if missing,
- it is set to infile+".filevector"}
+\item{outfile}{output filevector file name; if missing,
+it is set to infile+".filevector"}
- \item{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}
+\item{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}
- \item{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}
+\item{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}
- \item{skipcols}{how many columns of the input file to
- skip}
+\item{skipcols}{how many columns of the input file to skip}
- \item{skiprows}{how many rows of the input file to skip}
+\item{skiprows}{how many rows of the input file to skip}
- \item{transpose}{whether the file is to be transposed}
+\item{transpose}{whether the file is to be transposed}
- \item{R_matrix}{if true, the file format is assumed to
- follow the format of R data matrix produced with
- \code{write.table(...,col.names=TRUE,row.names=TRUE)}}
+\item{R_matrix}{if true, the file format is assumed to follow
+the format of R data matrix produced with
+\code{write.table(...,col.names=TRUE,row.names=TRUE)}}
- \item{type}{data DatABEL type to use ("DOUBLE", "FLOAT",
- "INT", "UNSIGNED_INT", "UNSIGNED_SHORT_INT", "SHORT_INT",
- "CHAR", "UNSIGNED_CHAR")}
+\item{type}{data DatABEL type to use ("DOUBLE", "FLOAT", "INT",
+"UNSIGNED_INT", "UNSIGNED_SHORT_INT", "SHORT_INT", "CHAR", "UNSIGNED_CHAR")}
- \item{cachesizeMb}{cache size for the resulting
- 'databel-class' object}
+\item{cachesizeMb}{cache size for the resulting 'databel-class' object}
- \item{readonly}{whether the resulting 'databel-class'
- object should be opened in readonly mode}
+\item{readonly}{whether the resulting 'databel-class' object should
+be opened in readonly mode}
- \item{naString}{the string used for missing data
- (default: NA)}
+\item{naString}{the string used for missing data (default: NA)}
- \item{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.}
+\item{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.}
}
\value{
The converted file is stored in the file system, a
-\link{databel-class} object connection to the file is
-returned.
+\link{databel-class} object connection to the file is returned.
}
\description{
-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
+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
+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
\code{write.table(...,col.names=TRUE,row.names=TRUE)}.
}
\examples{
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