[GenABEL-dev] [Genabel-commits] r1643 - pkg/DatABEL/man
Yurii Aulchenko
yurii.aulchenko at gmail.com
Sat Mar 15 14:58:26 CET 2014
Re: "needs to be checked"
check --as-cran
May be useful - they do check if docs are in good shape
Y
----------------------
Yurii Aulchenko
(sent from mobile device)
> On Mar 15, 2014, at 11:21 AM, "noreply at r-forge.r-project.org" <noreply at r-forge.r-project.org> wrote:
>
> Author: lckarssen
> Date: 2014-03-15 11:21:08 +0100 (Sat, 15 Mar 2014)
> New Revision: 1643
>
> Modified:
> pkg/DatABEL/man/DatABEL-package.Rd
> pkg/DatABEL/man/apply2dfo.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:
> Updated manual files for DatABEL after running Roxygen2. Only layout changes.
> I excluded databel-class.Rd, because it was missing a lot of \alias{} lines and had some other changes. Needs to be checked.
>
>
> Modified: pkg/DatABEL/man/DatABEL-package.Rd
> ===================================================================
> --- pkg/DatABEL/man/DatABEL-package.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/DatABEL-package.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -4,20 +4,20 @@
> \alias{DatABEL-package}
> \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)
> +Yurii Aulchenko (R code), Stepan Yakovenko (R and C++
> +code), Andrey Chernyh (C++ code)
> }
> \seealso{
> - \code{\link{apply2dfo}}, \code{\link{databel2matrix}},
> - \code{\link{databel2text}},
> - \code{\link{extract_text_file_columns}},
> - \code{\link{matrix2databel}}, \code{\link{text2databel}},
> - \code{\linkS4class{databel}}
> +\code{\link{apply2dfo}}, \code{\link{databel2matrix}},
> +\code{\link{databel2text}},
> +\code{\link{extract_text_file_columns}},
> +\code{\link{matrix2databel}}, \code{\link{text2databel}},
> +\code{\linkS4class{databel}}
> }
>
>
> Modified: pkg/DatABEL/man/apply2dfo.Rd
> ===================================================================
> --- pkg/DatABEL/man/apply2dfo.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/apply2dfo.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,22 +2,21 @@
> \alias{apply2dfo}
> \title{applies a function to 'databel' object}
> \usage{
> - apply2dfo(..., dfodata, anFUN = "lm", MAR = 2, procFUN,
> - outclass = "matrix", outfile, type = "DOUBLE",
> - transpose = TRUE)
> +apply2dfo(..., dfodata, anFUN = "lm", MAR = 2, procFUN,
> + outclass = "matrix", outfile, type = "DOUBLE", transpose = TRUE)
> }
> \arguments{
> \item{dfodata}{'databel' object which is iterated over}
>
> \item{anFUN}{user-defined analysis function}
>
> - \item{MAR}{which margin to iterate over (default = 2,
> - usually these are the 'columns' used to store SNP data)}
> + \item{MAR}{which margin to iteracte 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 one of the standard functions listed
> - below is used. Pre-defined processors included are
> + 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],
> @@ -26,9 +25,9 @@
> \item{outclass}{output to ("matrix" or "databel")}
>
> \item{outfile}{if output class is "databel", the
> - generated object is bound to the outfile}
> + generated object is bond to the outfile}
>
> - \item{type}{if output class is "databel", what data type
> + \item{type}{if output class is "databel", what data tyoe
> to use for storage}
>
> \item{transpose}{whether to transpose the output}
> @@ -36,47 +35,43 @@
> \item{...}{arguments passed to the anFUN}
> }
> \value{
> - A matrix (or 'databel'-matrix) containing results of
> - applying the function
> +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' object
> }
> \examples{
> -a <- matrix(rnorm(50), 10, 5)
> -rownames(a) <- paste("id", 1:10, sep="")
> -colnames(a) <- paste("snp", 1:5, sep="")
> -b <- as(a, "databel")
> -apply(a, FUN="sum", MAR=2)
> -apply2dfo(SNP, dfodata=b, anFUN="sum")
> -tA <- apply2dfo(SNP, dfodata=b, anFUN="sum",
> - outclass="databel", outfile="tmpA")
> +a <- matrix(rnorm(50),10,5)
> +rownames(a) <- paste("id",1:10,sep="")
> +colnames(a) <- paste("snp",1:5,sep="")
> +b <- as(a,"databel")
> +apply(a,FUN="sum",MAR=2)
> +apply2dfo(SNP,dfodata=b,anFUN="sum")
> +tA <- apply2dfo(SNP,dfodata=b,anFUN="sum",outclass="databel",outfile="tmpA")
> tA
> -as(tA, "matrix")
> -apply2dfo(SNP, dfodata=b, anFUN="sum", transpose=FALSE)
> -tB <- apply2dfo(SNP, dfodata=b, anFUN="sum", transpose=FALSE,
> - outclass="databel", outfile="tmpB")
> +as(tA,"matrix")
> +apply2dfo(SNP,dfodata=b,anFUN="sum",transpose=FALSE)
> +tB <- apply2dfo(SNP,dfodata=b,anFUN="sum",transpose=FALSE,outclass="databel",outfile="tmpB")
> tB
> -as(tB, "matrix")
> +as(tB,"matrix")
>
> -sex <- 1*(runif(10) > .5)
> -trait <- rnorm(10) + sex + as(b[, 2], "vector") + as(b[, 2], "vector") * sex * 5
> -apply2dfo(trait~SNP*sex, dfodata=b, anFUN="lm")
> -tC <- apply2dfo(trait~SNP*sex, dfodata=b, anFUN="lm",
> - outclass="databel", outfile="tmpC")
> +sex <- 1*(runif(10)>.5)
> +trait <- rnorm(10)+sex+as(b[,2],"vector")+as(b[,2],"vector")*sex*5
> +apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm")
> +tC <- apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",outclass="databel",outfile="tmpC")
> tC
> -as(tC, "matrix")
> -apply2dfo(trait~SNP*sex, dfodata=b, anFUN="lm", transpose=FALSE)
> -tD <- apply2dfo(trait~SNP*sex, dfodata=b, anFUN="lm", transpose=FALSE,
> - outclass="databel", outfile="tmpD")
> +as(tC,"matrix")
> +apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",transpose=FALSE)
> +tD <- apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",transpose=FALSE,outclass="databel",outfile="tmpD")
> tD
> -as(tD, "matrix")
> -rm(tA, tB, tC, tD)
> +as(tD,"matrix")
> +rm(tA,tB,tC,tD)
> gc()
> unlink("tmp*")
> }
> \author{
> - Yurii Aulchenko
> +Yurii Aulchenko
> }
>
>
> Modified: pkg/DatABEL/man/databel.Rd
> ===================================================================
> --- pkg/DatABEL/man/databel.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/databel.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,7 +2,7 @@
> \alias{databel}
> \title{initiates databel object}
> \usage{
> - databel(baseobject, cachesizeMb = 64, readonly = TRUE)
> +databel(baseobject, cachesizeMb = 64, readonly = TRUE)
> }
> \arguments{
> \item{baseobject}{name of the file or
> @@ -13,10 +13,10 @@
> \item{readonly}{readonly flag}
> }
> \description{
> - this is a simple wrapper for "new" function creating
> - databel object
> +this is a simple wrapper for "new" function creating
> +databel object
> }
> \author{
> - Yurii Aulchenko
> +Yurii Aulchenko
> }
>
>
> Modified: pkg/DatABEL/man/databel2matrix.Rd
> ===================================================================
> --- pkg/DatABEL/man/databel2matrix.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/databel2matrix.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,7 +2,7 @@
> \alias{databel2matrix}
> \title{converts 'databel' to matrix}
> \usage{
> - databel2matrix(from, rows, cols)
> +databel2matrix(from, rows, cols)
> }
> \arguments{
> \item{from}{'databel' matrix}
> @@ -12,15 +12,15 @@
> \item{cols}{which columns to include}
> }
> \value{
> - object of \code{\linkS4class{matrix}} class
> +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
> +Stepan Yakovenko
> }
>
>
> Modified: pkg/DatABEL/man/databel2text.Rd
> ===================================================================
> --- pkg/DatABEL/man/databel2text.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/databel2text.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,8 +2,8 @@
> \alias{databel2text}
> \title{Exports DatABEL object to a text file}
> \usage{
> - databel2text(databel, file, NAString = "NA",
> - row.names = TRUE, col.names = TRUE, transpose = FALSE)
> +databel2text(databel, file, NAString = "NA", row.names = TRUE,
> + col.names = TRUE, transpose = FALSE)
> }
> \arguments{
> \item{databel}{DatABEL object}
> @@ -19,9 +19,9 @@
> \item{transpose}{whether the matrix should be transposed}
> }
> \description{
> - Exports DatABEL object to a text file
> +Exports DatABEL object to a text file
> }
> \author{
> - Stepan Yakovenko
> +Stepan Yakovenko
> }
>
>
> Modified: pkg/DatABEL/man/extract_text_file_columns.Rd
> ===================================================================
> --- pkg/DatABEL/man/extract_text_file_columns.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/extract_text_file_columns.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,7 +2,7 @@
> \alias{extract_text_file_columns}
> \title{extracts columns from text file}
> \usage{
> - extract_text_file_columns(file, whichcols)
> +extract_text_file_columns(file, whichcols)
> }
> \arguments{
> \item{file}{file name}
> @@ -10,11 +10,11 @@
> \item{whichcols}{which columns to extract}
> }
> \value{
> - matrix of strings with values from that columns
> +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 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/get_temporary_file_name.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,7 +2,7 @@
> \alias{get_temporary_file_name}
> \title{generates temporary file name}
> \usage{
> - get_temporary_file_name(path = ".", withFVext = TRUE)
> +get_temporary_file_name(path = ".", withFVext = TRUE)
> }
> \arguments{
> \item{path}{path to directory where the temporary file
> @@ -12,6 +12,6 @@
> of *FVD and *FVI files too}
> }
> \description{
> - function to generate temporary file name
> +function to generate temporary file name
> }
>
>
> Modified: pkg/DatABEL/man/make_empty_fvf.Rd
> ===================================================================
> --- pkg/DatABEL/man/make_empty_fvf.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/make_empty_fvf.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,8 +2,8 @@
> \alias{make_empty_fvf}
> \title{makes empty filevector object}
> \usage{
> - make_empty_fvf(name, nvariables, nobservations,
> - type = "DOUBLE", cachesizeMb = 64, readonly = FALSE)
> +make_empty_fvf(name, nvariables, nobservations, type = "DOUBLE",
> + cachesizeMb = 64, readonly = FALSE)
> }
> \arguments{
> \item{name}{name fo the file to be assoiated with new
> @@ -24,10 +24,10 @@
> mode}
> }
> \value{
> - databel object; also file is created in file system
> +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 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/matrix2databel.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,8 +2,8 @@
> \alias{matrix2databel}
> \title{converts matrix to 'databel'}
> \usage{
> - matrix2databel(from, filename, cachesizeMb = 64,
> - type = "DOUBLE", readonly = FALSE)
> +matrix2databel(from, filename, cachesizeMb = 64, type = "DOUBLE",
> + readonly = FALSE)
> }
> \arguments{
> \item{from}{R matrix}
> @@ -21,15 +21,15 @@
> only mode}
> }
> \value{
> - object of class \code{\linkS4class{databel}}
> +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
> +Yurii Aulchenko
> }
>
>
> Modified: pkg/DatABEL/man/process_lm_output.Rd
> ===================================================================
> --- pkg/DatABEL/man/process_lm_output.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/process_lm_output.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -5,7 +5,7 @@
> \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",
> @@ -14,14 +14,14 @@
> \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 "sum", "prod", "sum_not_NA", "sum_NA")
> +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
> +"sum", "prod", "sum_not_NA", "sum_NA")
> }
> \examples{
> a <- matrix(rnorm(50),10,5)
> @@ -37,6 +37,6 @@
> apply2dfo(trait~SNP*sex,dfodata=b,anFUN="lm",procFUN="process_lm_output")
> }
> \seealso{
> - \link{apply2dfo}
> +\link{apply2dfo}
> }
>
>
> Modified: pkg/DatABEL/man/text2databel.Rd
> ===================================================================
> --- pkg/DatABEL/man/text2databel.Rd 2014-03-15 10:12:34 UTC (rev 1642)
> +++ pkg/DatABEL/man/text2databel.Rd 2014-03-15 10:21:08 UTC (rev 1643)
> @@ -2,16 +2,16 @@
> \alias{text2databel}
> \title{converts text file to filevector format}
> \usage{
> - text2databel(infile, outfile, colnames, rownames,
> - skipcols, skiprows, transpose = FALSE,
> - R_matrix = FALSE, type = "DOUBLE", cachesizeMb = 64,
> - readonly = TRUE, naString = "NA")
> +text2databel(infile, outfile, colnames, rownames, skipcols, skiprows,
> + transpose = FALSE, R_matrix = FALSE, type = "DOUBLE",
> + cachesizeMb = 64, readonly = TRUE, naString = "NA",
> + unlinkTmpTransposeFiles = TRUE)
> }
> \arguments{
> \item{infile}{input text file name}
>
> \item{outfile}{output filevector file name; if missing,
> - it is set to infile + ".filevector"}
> + it is set to infile+".filevector"}
>
> \item{colnames}{where are the column names stored? If
> missing, no column names; if integer, this denotes the
> @@ -48,33 +48,38 @@
>
> \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.}
> }
> \value{
> - The converted file is stored in the file system, a
> - \link{databel-class} object connection to the file is
> - returned.
> +The converted file is stored in the file system, a
> +\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 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
> - \code{write.table(..., col.names=TRUE, row.names=TRUE)}.
> +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
> +\code{write.table(...,col.names=TRUE,row.names=TRUE)}.
> }
> \examples{
> -cat("this is an example which you can run if you can write to the file system\\n")
> +cat("this is an example which you can run if you can write to the
> +file system\\n")
>
> \dontrun{
>
> @@ -82,19 +87,19 @@
> 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="")
> +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.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")
>
> @@ -107,25 +112,28 @@
>
> # convert text two filevector format
>
> -text2databel(infile="test_matrix_NOnames.dat", outfile="test_matrix_NOnames.fvf",
> +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",
> +text2databel(infile="test_matrix_NOnames.dat",
> + outfile="test_matrix_NOnames_T.fvf",
> colnames="test_matrix.colnames",
> - rownames="test_matrix.rownames",
> - transpose=TRUE)
> + 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",
> +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",
> +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")
> @@ -144,7 +152,8 @@
> 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",
> +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")
> @@ -152,5 +161,6 @@
> }
> }
> \author{
> - Yurii Aulchenko
> +Yurii Aulchenko
> }
> +
>
> _______________________________________________
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