[Genabel-commits] r1643 - pkg/DatABEL/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Mar 15 11:21:08 CET 2014
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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