daizhenwei / bdmmacorrect

Batch effect correction for microbiome data with Bayesian Dirichlet-multinomial regression

Our project developed a Bayesian approach to correct for batch effects in microbiome compositional data with Dirichlet-Multinomial regression.

References

Dai, Z., Wong, S. H., Yu, J., & Wei, Y. (2019). Batch effects correction for microbiome data with Dirichlet-multinomial regression. Bioinformatics. Bioinformatics, 35 (5): 807–814

bdmmacorrect's Issues

building error

Hi there! Thanks for the good work. Is it on bioconductor yet?

I was trying out your tool on some data, but encountered this error below. I was thinking the key error is the build thing rather the RcppEigen warnings

install_github("DAIZHENWEI/BDMMAcorrect")

Installing package into ‘/Users/ayo/Library/R/3.5/library’
(as ‘lib’ is unspecified)

• installing source package ‘BDMMAcorrect’ ...
  ** libs
  clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/ayo/Library/R/3.5/library/Rcpp/include" -I"/Users/ayo/Library/R/3.5/library/RcppArmadillo/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include" -I/usr/local/include -DARMA_DONT_USE_OPENMP -fPIC -Wall -g -O2 -c MCMC_algorithm.cpp -o MCMC_algorithm.o

In file included from RcppExports.cpp:5:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/RcppEigen.h:25:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/RcppEigenForward.h:40:
In file included from /Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported/Eigen/SparseExtra:51:
/Library/Frameworks/R.framework/Versions/3.5/Resources/library/RcppEigen/include/unsupported/Eigen/../../Eigen/src/Core/util/ReenableStupidWarnings.h:10:30: warning: pragma diagnostic pop could not pop, no matching push [-Wunknown-pragmas]
#pragma clang diagnostic pop
^
17 warnings generated.
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o BDMMAcorrect.so MCMC_algorithm.o RcppExports.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -g -O2 -msse2 -mfpmath=sse -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: library not found for -lgfortran
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [BDMMAcorrect.so] Error 1
ERROR: compilation failed for package ‘BDMMAcorrect’

• removing ‘/Users/ayo/Library/R/3.5/library/BDMMAcorrect’
  Error in i.p(...) :
  (converted from warning) installation of package ‘/var/folders/zs/2snw_1694fb300jsl3vf2jwm0000gp/T//RtmpGlb8P3/file4a363125c7d7/BDMMAcorrect_0.99.39.tar.gz’ had non-zero exit status

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base

other attached packages:
[1] usethis_1.4.0 devtools_2.0.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.19 rstudioapi_0.8 magrittr_1.5
[4] pkgload_1.0.2 R6_2.3.0 rlang_0.3.0.1
[7] tools_3.5.1 pkgbuild_1.0.2 sessioninfo_1.1.1
[10] cli_1.0.1 withr_2.1.2 remotes_2.0.2
[13] assertthat_0.2.0 digest_0.6.18 rprojroot_1.3-2
[16] crayon_1.3.4 processx_3.2.0 callr_3.0.0
[19] base64enc_0.1-3 fs_1.2.6 ps_1.2.0
[22] curl_3.2 memoise_1.1.0 glue_1.3.0
[25] compiler_3.5.1 desc_1.2.0 backports_1.1.2
[28] prettyunits_1.0.2

Many Thanks

Variables class

Hi, I'm trying to use your method to asses for differences in hypertensive groups.

For the moment I would like to not add a confounder variable, is it possible?

As I noticed that apparently I needed to add a confounder variable, I added a categorical confounder, but I got the next error:

Error in colMeans(X) : 'x' must be numeric

So, is it necessary to add a numeric confounder? And what happens when I have confounders of both types: categorical and continuous?

Thanks for you time, and for this great tool