lfa

Logistic factor analysis

Installation

To install latest version on Bioconductor, open R and type:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("lfa")

You can also install development version from GitHub this way:

install.packages("devtools")
library("devtools")
install_github("Storeylab/lfa")

Apple OS X users, see Troubleshooting below.

Data input

We recommend using the genio or BEDMatrix packages to read genotype data into an R matrix.

Be warned that genotype matrices from genio and some lfa functions require a lot of memory. As a rule of thumb, the in memory sizes of a few relevant genotype matrices:

431345 SNPs by 940 individuals: 1.5 GB needed for genotype matrix, about 9 GB to run lfa.
339100 SNPs by 1500 individuals: 1.9 GB needed for genotype matrix, about 11.5 GB to run lfa.

BEDMatrix inputs consume much less memory but can be slower otherwise.

Troubleshooting

Apple OS X users may experience a problem due to Fortran code that is included in this package. You must install the X code command line tools (XCode CLI) and gfortran. Try the following commands on terminal:

xcode-select --install 
brew install gcc

If XCode installation fails, you may have to sign up on Apple Developer: https://www.ics.uci.edu/~pattis/common/handouts/macmingweclipse/allexperimental/macxcodecommandlinetools.html

Alternatively, this Installer Package for macOS R toolchain may work https://github.com/rmacoslib/r-macos-rtools/

Citations

Hao, Wei, Minsun Song, and John D. Storey. "Probabilistic Models of Genetic Variation in Structured Populations Applied to Global Human Studies." Bioinformatics 32, no. 5 (March 1, 2016): 713–21. doi:10.1093/bioinformatics/btv641. arXiv.

1.28.2: compile error

OS: Arch Linux
R version: 4.3.0
Build details: https://github.com/BioArchLinux/Packages/blob/master/BioArchLinux/r-lfa/PKGBUILD
Full log: https://build.bioarchlinux.org/api/pkg/r-lfa/log/1682143284

* installing *source* package ‘lfa’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 12.2.1 20230201’
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c fastmat.c -o fastmat.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c lfa-init.c -o lfa-init.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c lfa.c -o lfa.o
gcc -I"/usr/include/R/" -DNDEBUG   -I/usr/local/include    -fpic  -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -fexceptions         -Wp,-D_FORTIFY_SOURCE=2 -Wformat -Werror=format-security         -fstack-clash-protection -fcf-protection -g -ffile-prefix-map=/build/r/src=/usr/src/debug/r -flto=auto -ffat-lto-objects  -c lreg.c -o lreg.o
In file included from /usr/include/R/R.h:78,
                 from lfa.h:4,
                 from fastmat.c:1:
fastmat.c: In function ‘mv’:
fastmat.c:22:14: error: too few arguments to function ‘dgemv_’
   22 |     F77_CALL(dgemv)(&tr,dimA,dimA+1,&alpha,A,dimA,v,&one,&zero,ret,&one);
      |              ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
fastmat.c: In function ‘tmv’:
fastmat.c:48:14: error: too few arguments to function ‘dgemv_’
   48 |     F77_CALL(dgemv)(&tr,dimA,dimA+1,&alpha,A,dimA,v,&one,&zero,ret,&one);
      |              ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:191: fastmat.o] Error 1
make: *** Waiting for unfinished jobs....
In file included from /usr/include/R/R.h:78,
                 from lfa.h:4,
                 from lreg.c:1:
lreg.c: In function ‘lreg’:
lreg.c:49:18: error: too few arguments to function ‘dgemv_’
   49 |         F77_CALL(dgemv)(&tr,dimX,dimX+1,&alpha,X,dimX,b,&ione,&zero,p,&ione);
      |                  ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
lreg.c:120:18: error: too few arguments to function ‘dgemv_’
  120 |         F77_CALL(dgemv)(&tr,dimX+1,dimX+1,&one,w,dimX+1,f,&ione,&one,b,&ione);
      |                  ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:10: note: declared here
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      |          ^~~~~
/usr/include/R/R_ext/RS.h:77:25: note: in definition of macro ‘F77_CALL’
   77 | # define F77_CALL(x)    x ## _
      |                         ^
/usr/include/R/R_ext/BLAS.h:107:1: note: in expansion of macro ‘F77_NAME’
  107 | F77_NAME(dgemv)(const char *trans, const int *m, const int *n,
      | ^~~~~~~~
make: *** [/usr/lib64/R/etc/Makeconf:191: lreg.o] Error 1
ERROR: compilation failed for package ‘lfa’
* removing ‘/build/r-lfa/src/lfa’
* restoring previous ‘/build/r-lfa/src/lfa’

storeylab / lfa Goto Github PK

lfa's Introduction

lfa

Installation

Data input

Troubleshooting

Citations

lfa's People

Contributors

Stargazers

Watchers

Forkers

lfa's Issues

fix factors

1.28.2: compile error

trunc.svd and center not export

Recommend Projects

React

Vue.js

Typescript

TensorFlow

Django

Laravel

D3

Recommend Topics

javascript

web

server

Machine learning

Visualization

Game

Recommend Org

Facebook

Microsoft

Google

Alibaba

D3

Tencent