[GenABEL-dev] [Genabel-commits] r1643 - pkg/DatABEL/man
L.C. Karssen
lennart at karssen.org
Sat Mar 15 17:43:30 CET 2014
Will do!
I've updated the makedistrib_DatABEL.sh script some time ago to add that
check as well.
With that databel-class.Rd I noticed that roxygen2 had remove a lot of
things from the .Rd file. So it's something that I need to check in more
detail. Also roxygen2 has reduced the NAMESPACE file to one line:
exportClasses(databel)
Another thing that I need to check before attempting an upload.
Best,
Lennart.
On 15-03-14 14:58, Yurii Aulchenko wrote:
> 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
>> }
>> +
>>
>> _______________________________________________
>> Genabel-commits mailing list
>> Genabel-commits at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
> _______________________________________________
> genabel-devel mailing list
> genabel-devel at lists.r-forge.r-project.org
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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