Last updated: 2020-05-25

Checks: 7 0

Knit directory: analysis_pipelines/

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Repository version: 94a32c0

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Rmd 94a32c0 kevinlkx 2020-05-25 wflow_publish(“analysis/twas_fusion_pipeline.Rmd”)

Install the FUSION software

FUSION software is implemented in R. Installation is easy: simply download and unpack the FUSION software package from github: https://github.com/gusevlab/fusion_twas

wget https://github.com/gusevlab/fusion_twas/archive/master.zip
unzip master.zip
cd fusion_twas-master

Then, install required libraries.

install.packages(c('optparse','RColorBrewer'))
install.packages('plink2R-master/plink2R/',repos=NULL)
install.packages(c('glmnet','methods'))

Please see the detail instructions: http://gusevlab.org/projects/fusion/

Run TWAS analysis

FUSION website (http://gusevlab.org/projects/fusion/) provides very detailed instructions and examples to run TWAS analysis, compute your own weights, and conditional analysis, etc.


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] workflowr_1.6.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        rprojroot_1.3-2   digest_0.6.23     later_1.0.0      
 [5] R6_2.4.1          backports_1.1.5   git2r_0.26.1.9000 magrittr_1.5     
 [9] evaluate_0.14     stringi_1.4.5     rlang_0.4.4       fs_1.3.1         
[13] promises_1.1.0    whisker_0.4       rmarkdown_2.1     tools_3.5.1      
[17] stringr_1.4.0     glue_1.3.1        httpuv_1.5.2      xfun_0.12        
[21] yaml_2.2.0        compiler_3.5.1    htmltools_0.4.0   knitr_1.28