Last updated: 2018-05-15
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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.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | e05bc83 | LSun | 2018-05-12 | Update to 1.0 |
| Rmd | cc0ab83 | Lei Sun | 2018-05-11 | update |
| html | 0f36d99 | LSun | 2017-12-21 | Build site. |
| html | 853a484 | LSun | 2017-11-07 | Build site. |
| Rmd | 894c395 | LSun | 2017-03-07 | histogram |
| html | 894c395 | LSun | 2017-03-07 | histogram |
| Rmd | 03366d9 | LSun | 2017-03-06 | correlated_z |
| html | 03366d9 | LSun | 2017-03-06 | correlated_z |
| Rmd | def3da5 | LSun | 2017-03-06 | correlated z |
| html | def3da5 | LSun | 2017-03-06 | correlated z |
Last updated: 2018-05-15
Code version: 388e65e
Efron 2010 and Schwartzman’s comment brings to the center the question “what’s the behavior of \(z\) scores under correlation?” Schwartzman pointed out in theory that “the observed histogram is more likely to be narrow than wide, and that it cannot be too wide before it becomes bimodal.” Let’s take a look if this result holds true under our simulation scheme with GTex/Liver data.
z = read.table("../output/z_null_liver_777.txt")
We randomly selected 20 data sets, each with \(10000\) z scores, generated by the null simulation pipeline. Based on each data set we plot two histograms, one using default number of bins and the other \(100\) bins. The red line indicates the density of \(N(0, 1)\).
set.seed(777)
sample_z = sort(sample(dim(z)[1], 20))
x = seq(- 10, 10, 0.01)
y = dnorm(x)
for (i in sample_z) {
cat("Data Set", i)
hist(as.numeric(z[i, ]), xlab = "z scores", freq = FALSE, ylim = c(0, 0.45), main = "10000 z scores, default")
lines(x, y, col = "red")
hist(as.numeric(z[i, ]), xlab = "z scores", freq = FALSE, ylim = c(0, 0.45), nclass = 100, main = "10000 z scores, 100 bins")
lines(x, y, col = "red")
}
Data Set 11

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 103

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 171

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 247

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 343

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 345

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 347

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 383

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 412

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 492

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 574

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 588

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 654

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 688

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 693

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 726

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 853

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 855

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 942

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |
Data Set 993

| Version | Author | Date |
|---|---|---|
| 0f36d99 | LSun | 2017-12-21 |
| 03366d9 | LSun | 2017-03-06 |
| def3da5 | LSun | 2017-03-06 |

sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/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_1.0.1 Rcpp_0.12.16 digest_0.6.15
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.21.0 magrittr_1.5 evaluate_0.10.1
[10] stringi_1.1.6 whisker_0.3-2 R.oo_1.21.0
[13] R.utils_2.6.0 rmarkdown_1.9 tools_3.4.3
[16] stringr_1.3.0 yaml_2.1.18 compiler_3.4.3
[19] htmltools_0.3.6 knitr_1.20
This reproducible R Markdown analysis was created with workflowr 1.0.1