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# packages in environment at /project2/xinhe/yanyul/softwares/Anaconda2/envs/deepvarpred_test:
#
bedtools                  2.25.0                        2    bioconda
bzip2                     1.0.6                         1    conda-forge
ca-certificates           2017.1.23                     0    conda-forge
cairo                     1.14.8                        0
certifi                   2017.1.23                py35_0    conda-forge
cffi                      1.7.0                    py35_0    conda-forge
cryptography              1.7.1                    py35_0
curl                      7.52.1                        0    conda-forge

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sapply(list.files('path-to-folder', '*.R', full.names = T), source)

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import argparse

parser = argparse.ArgumentParser(description='generate script from template')
parser.add_argument('word', metavar='KEY=VALUE', type=str, nargs='+',
                   help='key-value pairs')
parser.add_argument('--template', metavar='input filename', type=str,
                   help='template file')
parser.add_argument('--output', metavar='output filename', type=str,
                   help='output')

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zval2pval = function(z) {
  exp(pnorm(abs(z), log.p=T, low=F)) * 2
}

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compute_auc = function(curve) {
  # f = curve %>% filter(nTP > 0) %>% group_by(nTP) %>% summarize(y = mean(tpr), x = fpr[1] - fpr[2])
  o1 = rbind(c(1, 1), curve %>% select(tpr, fpr))
  o2 = rbind(curve %>% select(tpr, fpr), c(0, 0))
  # message('e')
  y = data.frame(x1 = o1$fpr, x2 = o2$fpr, y1 = o1$tpr, y2 = o2$tpr) 
  e = y %>% mutate(s = (x1 - x2) * (y1 + y2) / 2)
  data.frame(roc_auc = sum(e$s))
}

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my_qqplot_by_group <- function(pval, group, ...) {
  n <- length(pval)
  pexp <- rank(pval) / n
  df <- data.frame(p.val = pval, p.exp = pexp, grp = group)
  p <- ggplot(df) + geom_point(aes(x = -log10(p.exp), y = -log10(p.val), color = grp), ...) + geom_hline(yintercept = -log10(0.05 / n)) + theme_bw() + geom_abline(slope = 1, intercept = 0, linetype = 2)
  return(p)
}

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Dependency

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

locale:
[1] C

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set.seed(100)
# p1 = runif(1000)
# p2 = runif(5)
z = rep(rnorm(10000))
z[sample(1:10000, size = 3, replace = F)] = rnorm(3, 7, sd = 1)
# plot(-log10(p))
zobs = rep(0, 10000)
density = exp(c(-5:-1, 0, -1:-5)*0.5)
for(i in 6 : 9995) {
  zobs[i] = sum(density * z[c(i-(5:1),i,i+(1:5))])

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th = theme(panel.border = element_blank(), panel.grid.major = element_blank(),panel.grid.minor = element_blank(), axis.line = element_line(colour = "#170a45", size = .5), axis.ticks = element_line(colour = "#170a45", size = .2), axis.text = element_text(color = '#170a45'))
th2 = th
th2$panel.border = element_rect(colour = th2$axis.line$colour)

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mymixer = c(
  'splicing observed' = rgb(200, 90, 40, maxColorValue = 255),
  'expression observed' = rgb(42, 155, 204, maxColorValue = 255),
  'splicing shuffled' = 'gray',
  'expression shuffled' = 'gray'
)