privefl

urls <- gsubfn::strapply(
  readLines("https://datadryad.org//resource/doi:10.5061/dryad.ns8q3"),
  "<a href=\"(/bitstream/handle/10255/dryad\\.[0-9]+/meta_chr_[0-9]+\\?sequence=1)\">",
  simplify = 'c')

sumstats <- purrr::map_dfr(urls, ~ {
  download.file(paste0("https://datadryad.org", .x),
                destfile = (tmp <- tempfile(fileext = ".txt")))
  sumstats <- bigreadr::fread2(
    tmp, select = c("chromosome", "position", "a0", "a1",

privefl

sapply(list.files(pattern = "\\.html$"), function(file) {
  html <- readLines(file)
  new_html <- gsub(
    "https:.*?MathJax\\.js\\?",
    "https://mathjax.rstudio.com/latest/MathJax.js?", 
    html
  )
  writeLines(new_html, file)
})

privefl

library(Matrix)

X <- rsparsematrix(1e4, 1e4, density = 0.01)

system.time(
  test <- apply(X, 1, mean)
)

system.time(
  test2 <- rowMeans(X)

privefl

require("bigstatsr")

#' Get genes
#'
#' Get genes associated with SNPs.
#'
#' @param rsid A character vector of 'rs' ID of SNPs to investigate.
#' @param ncores Number of cores to use.
#'
#' @return A character vector of genes in the form `"<name>:<ID>". Note that

privefl

MY_THEME <- function(p, coeff = 1) {
  p + theme_bw() +
    theme(plot.title    = element_text(size = rel(2.0 * coeff), hjust = 0.5),
          plot.subtitle = element_text(size = rel(1.5 * coeff), hjust = 0.5),
          legend.title  = element_text(size = rel(1.8 * coeff)),
          legend.text   = element_text(size = rel(1.3 * coeff)),
          axis.title    = element_text(size = rel(1.5 * coeff)),
          axis.text     = element_text(size = rel(1.2 * coeff)),
          legend.key.height = unit(1.3 * coeff, "line"),
          legend.key.width = unit(1.3 * coeff, "line"))

privefl

library(dplyr)
# dplyr programming
my_summarise <- function(df, group) {
  group <- enquo(group)
  
  df %>%
    group_by(!!group) %>%
    summarise_all(mean)
}

privefl

library(dplyr)
# dplyr programming
my_summarise <- function(df, group) {
  group <- enquo(group)
  
  df %>%
    group_by(!!group) %>%
    summarise_all(mean)
}

privefl

library(dplyr)
# dplyr programming
my_summarise <- function(df, group) {
  group <- enquo(group)
  
  df %>%
    group_by(!!group) %>%
    summarise_all(mean)
}

privefl

library(dplyr)
# dplyr programming
my_summarise <- function(df, group) {
  group <- enquo(group)
  
  df %>%
    group_by(!!group) %>%
    summarise_all(mean)
}

privefl

#### IN ORDER ####
# In first session, run:
write(1, "test.txt")
obj.lock <- flock::lock("test.txt")

# In second session, run this (this will wait the unlock in the first session)
obj.lock <- flock::lock("test.txt")
write(2, "test.txt", append = TRUE)
flock::unlock(obj.lock)