enrichment

Last updated: 2019-02-14

• ✖ R Markdown file: uncommitted changes

  The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

• ✔ Environment: empty

  Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

• ✔ Seed: set.seed(20181119)

  The command set.seed(20181119) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

• ✔ Session information: recorded

  Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

• ✔ Repository version: fcaa341

  Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
  
  Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

  
  Ignored files:
      Ignored:    .Rproj.user/
  
  Untracked files:
      Untracked:  analysis/enrichment.Rmd
      Untracked:  data/SNP_200000.txt
      Untracked:  data/SNP_50000.txt
      Untracked:  data/SNP_500000.txt
  
  Unstaged changes:
      Modified:   .gitignore
      Modified:   analysis/index.Rmd
  
  

  Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

module load mysql
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e '
select
 K.name2,
 K.name,
 S.name,
 S.avHet,
 S.chrom,
 S.chromStart,
 K.txStart,
 K.txEnd
from snp150 as S
left join refGene as K on
 (S.chrom=K.chrom and not(K.txEnd+50000<S.chromStart or S.chromEnd+50000<K.txStart))
where
 S.name in ("rs7148456","rs12895055","rs7170068","rs520843","rs12716973","rs2192932","rs17200916","rs1198588","rs324017","rs4151680","rs301791","rs324015","rs9882911","rs11633075","rs2027349","rs186132169","rs9661794","rs7936858","rs3861678","rs10933","rs6071578")' > /project2/xinhe/simingz/CROP-seq/cropseq/data/SNP_50000.txt

SNPfile <- "/project2/xinhe/simingz/CROP-seq/scRNA_seq_SNP_list.txt"
SNPs <- read.table(SNPfile, header=F, stringsAsFactors = F)
cisgene <- read.table("data/SNP_50000.txt", stringsAsFactors = F,sep="\t", header=T)

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     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_1.0.0        digest_0.6.18    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.23.0      magrittr_1.5      evaluate_0.12    
[10] stringi_1.2.4     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20       

This reproducible R Markdown analysis was created with workflowr 1.1.1