DatABEL: File-Based Access to Large Matrices Stored on HDD in Binary Format

Provides an interface to the C++ FILEVECTOR library facilitating analysis using large (giga- to tera-bytes) matrices. Matrix storage is organized in a way that either columns or rows are quickly accessible. DatABEL is primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL.

Install the latest version of this package by entering the following in R:
install.packages("DatABEL")
AuthorYurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar, Maksim Struchalin, Lennart C. Karssen
Date of publication2015-03-31 07:46:13
MaintainerLennart Karssen <lennart@karssen.org>
LicenseGPL (>= 2)
Version0.9-6

View on CRAN

Functions

apply2dfo Man page
backingfilename Man page
backingfilename,databel-method Man page
cachesizeMb Man page
cachesizeMb<- Man page
cachesizeMb<-,databel-method Man page
cachesizeMb,databel-method Man page
connect Man page
connect,databel-method Man page
databel Man page
"DatABEL" Man page
databel2matrix Man page
databel2text Man page
databel-class Man page
[<-,databel-method Man page
[,databel-method Man page
DatABEL-package Man page
dim,databel-method Man page
dimnames<-,databel-method Man page
dimnames,databel-method Man page
disconnect Man page
disconnect,databel-method Man page
extract_text_file_columns Man page
get_dimnames Man page
get_dimnames,databel-method Man page
get_temporary_file_name Man page
length,databel-method Man page
make_empty_fvf Man page
matrix2databel Man page
.onLoad Man page
process_lm_output Man page
process_simple_output Man page
save_as Man page
save_as,databel-method Man page
set_dimnames<- Man page
set_dimnames<-,databel-method Man page
setReadOnly<- Man page
setReadOnly<-,databel-method Man page
show,databel-method Man page
sum_NA Man page
sum_not_NA Man page
text2databel Man page

Files

TODO
inst
inst/doc
inst/doc/intro_DatABEL.R
inst/doc/intro_DatABEL.pdf
inst/doc/intro_DatABEL.Rnw
inst/unitTests
inst/unitTests/runit.text2databel.R
inst/unitTests/reportSummary.txt
inst/unitTests/Makefile
inst/unitTests/runit.databel_class.R
inst/unitTests/report.html
inst/unitTests/runit.many_objects.R
inst/unitTests/report.txt
inst/unitTests/mytest_iterator.R inst/unitTests/runit.NAN_test.R inst/unitTests/runit.generate_and_read_small_files.R inst/unitTests/runit.iterator.R inst/unitTests/runit.apply2dfo.R inst/unitTests/runit.read_large_file.R inst/unitTests/shared_functions.R
src
src/AbstractMatrix_R.cpp
src/Makevars
src/RealHandlerWrapper.cpp
src/AbstractMatrix.cpp
src/Transposer.h
src/FileVector.cpp
src/ReusableFileHandle.cpp
src/frutil.cpp
src/dautil.cpp
src/Rstuff.h
src/frversion.h
src/frutil.h
src/FileVector.h
src/Logger.h
src/CastUtils.cpp
src/dautil.h
src/ReusableFileHandle.h
src/FilteredMatrix.cpp
src/FilteredMatrix_R.cpp
src/iterator.cpp
src/const.h
src/iterator_functions.h
src/AbstractMatrix.h
src/CastUtils.h
src/RealHandlerWrapper.h
src/Logger.cpp
src/convert_util.h
src/Transposer.cpp
src/iterator_functions.cpp
src/convert_util.cpp
src/FilteredMatrix.h
NAMESPACE
R
R/databel_class.R R/databel_internal.R R/databel_class_internal.R R/databel2text.R R/databel2matrix.R R/extract_text_file_columns.R R/DatABEL-package.R R/make_empty_fvf.R R/get_temporary_file_name.R R/matrix2databel.R R/apply2dfo_util.R R/text2databel.R R/databel.R R/apply2dfo.R R/zzz.R
vignettes
vignettes/intro_DatABEL.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
ChangeLog
man
man/databel2text.Rd man/get_temporary_file_name.Rd man/extract_text_file_columns.Rd man/databel-class.Rd man/databel2matrix.Rd man/apply2dfo.Rd man/DatABEL-internal.Rd man/matrix2databel.Rd man/process_lm_output.Rd man/text2databel.Rd man/make_empty_fvf.Rd man/DatABEL-package.Rd man/databel.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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