Florian Privé privefl
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| 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
/ apply-sp.R
Created
July 13, 2018 08:51
Example of efficiently using "`apply`" with a sparse matrix in R.
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| library(Matrix) | |
| X <- rsparsematrix(1e4, 1e4, density = 0.01) | |
| system.time( | |
| test <- apply(X, 1, mean) | |
| ) | |
| system.time( | |
| test2 <- rowMeans(X) |
privefl
/ change-mathjax.R
Created
October 4, 2018 16:27
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| 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) | |
| }) |
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| 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", |
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