Last updated: 2020-01-13

Checks: 5 1

Knit directory: hgen471/

This reproducible R Markdown analysis was created with workflowr (version 1.3.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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(20200105)

The command set.seed(20200105) 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

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Cache: none

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Repository version: 1db3089

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Ignored files:
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    docs/.DS_Store

Untracked files:
    Untracked:  analysis/L1-miscel.Rmd
    Untracked:  analysis/L3-Crohns-Additive.Rmd

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Crohns additive test of association with rs11957134

m = matrix(c(341,395,3151,5467),nrow=2)
row.names(m) = c("crohns","control")
colnames(m) = c("A","G")
print(m)
          A    G
crohns  341 3151
control 395 5467
chisq.test(m)

    Pearson's Chi-squared test with Yates' continuity correction

data:  m
X-squared = 27.242, df = 1, p-value = 1.795e-07
fisher.test(m)

    Fisher's Exact Test for Count Data

data:  m
p-value = 2.287e-07
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 1.283301 1.747461
sample estimates:
odds ratio 
  1.497685

example when chi2 approximation fails

m = matrix(c(11,0,31,54),nrow=2)
row.names(m) = c("crohns","control")
colnames(m) = c("A","G")
print(m)
         A  G
crohns  11 31
control  0 54
chisq.test(m)$p.value
Warning in chisq.test(m): Chi-squared approximation may be incorrect
[1] 0.0002390852
fisher.test(m)$p.value
[1] 4.853876e-05
chisq.test(m)$p.value/fisher.test(m)$p.value
Warning in chisq.test(m): Chi-squared approximation may be incorrect
[1] 4.925656

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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

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

loaded via a namespace (and not attached):
 [1] workflowr_1.3.0 Rcpp_1.0.2      digest_0.6.19   rprojroot_1.3-2
 [5] backports_1.1.4 git2r_0.25.2    magrittr_1.5    evaluate_0.14  
 [9] rlang_0.4.1     stringi_1.4.3   fs_1.3.1        rmarkdown_1.13 
[13] tools_3.6.0     stringr_1.4.0   glue_1.3.1      xfun_0.7       
[17] yaml_2.2.0      compiler_3.6.0  htmltools_0.4.0 knitr_1.23