aSPU

Package: aSPU
Version: 1.42
Date: 2016-5-2
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU')
tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests
and gene-based and some pathway based association tests (Pathway based Sum of
Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU'
test for multiple traits - single 'SNP' (single-nucleotide-polymorphism)
association in generalized estimation equations, 'MTaSPUs' test for multiple
traits - single 'SNP' association with Genome Wide Association Studies ('GWAS')
summary statistics, Gene-based Association Test that uses an extended Simes
procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version
of 'GATES' test for pathway-based association testing ('GATES-Simes'). ).
The tests can be used with genetic and other data sets with covariates. The
response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set
association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP'
set association with summary statistics ('aSPUs'), (3) Single trait-pathway
association with individual-level data ('aSPUpath'), (4) Single trait-pathway
association with summary statistics ('aSPUsPath'), (5) Multiple traits-single
'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-
single SNP association with summary statistics ('MTaSPUs'), (7) Multiple traits-`SNP' set association with summary statistics(`MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics(`MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Suggests: knitr
VignetteBuilder: knitr
Imports: Rcpp (>= 0.12.1)
Depends: R (>= 3.1.0), gee, MASS, mvtnorm, fields, matrixStats
License: GPL-3
LinkingTo: Rcpp, RcppArmadillo
URL: https://github.com/ikwak2/aSPU
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-02 17:30:10 UTC; ikwak
Repository: CRAN
Date/Publication: 2016-05-03 02:08:52

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'aSPU' ...
** package 'aSPU' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c R_get_pv.c -o R_get_pv.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c R_get_pvs.c -o R_get_pvs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c R_get_pvs2.c -o R_get_pvs2.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c aSPU.cpp -o aSPU.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include" -I"/home/ddbj/local/lib64/R/library/RcppArmadillo/include"   -fpic  -g -O2  -c util.c -o util.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o aSPU.so R_get_pv.o R_get_pvs.o R_get_pvs2.o RcppExports.o aSPU.o util.o -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/aSPU/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'aSPU'
    finding HTML links ... done
    GATES2                                  html  
    GEEaSPU                                 html  
    GatesSimes                              html  
    Hyst                                    html  
    MTaSPUs                                 html  
    MTaSPUsSet                              html  
    MTaSPUsSetC                             html  
    MTaSPUsSetPath                          html  
    MTaSPUsSetScore                         html  
    SAMD11                                  html  
    aSPU                                    html  
    aSPUpath                                html  
    aSPUs                                   html  
    aSPUsPath                               html  
    aSPUw                                   html  
    estcov                                  html  
    exdat                                   html  
    getlogitp                               html  
    kegg9                                   html  
    minP                                    html  
    simPathAR1Snp                           html  
    someGs                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (aSPU)
Making 'packages.html' ... done