mikelove

accession2url <- function(x) {
  prefix <- "ftp://ftp.sra.ebi.ac.uk/vol1/fastq"
  dir1 <- paste0("/",substr(x,1,6))
  dir2 <- ifelse(nchar(x) == 9, "",
          ifelse(nchar(x) == 10, paste0("/00",substr(x,10,10)),
          ifelse(nchar(x) == 11, paste0("/0",substr(x,10,11)),
                                 paste0("/",substr(x,10,12)))))
  paste0(prefix,dir1,dir2,"/",x)
}

mikelove

nrep <- 100
d <- expand.grid(n=c(3,5,10,20), sd=c(1,2,3))
d <- d[rep(seq_len(nrow(d)),each=nrep),]

simulate <- function(n, sd) {
  rnorm(n=n, mean=0, sd=sd)
}

library(purrr)
library(dplyr)

mikelove

• xcode
• iterm2
• source code pro / fire mono
• homebrew
• zsh
• git
• emacs & ESS
• R & Rstudio
• mactex
• ispell

mikelove

n <- 50
m <- 40
m_inform <- 10
set.seed(1)
niter <- 200
intradist <- numeric(niter)
interdist <- numeric(niter)
mus <- seq(from=0, to=3, length=niter)
library(Rtsne)
cols <- rep(1:2, each=n/2)

mikelove

perl -pe 's|\\Robject{(.+?)}|`\1`|g' | 
perl -pe 's|\\Rcode{(.+?)}|`\1`|g' | 
perl -pe 's|\\Rclass{(.+?)}|*\1*|g' |
perl -pe 's|\\Rfunction{(.+?)}|*\1*|g' |
perl -pe 's|\\texttt{(.+?)}|`\1`|g' |
perl -pe 's|\\textit{(.+?)}|*\1*|g' |
perl -pe 's|\\textbf{(.+?)}|**\1**|g' |
perl -pe 's|\\emph{(.+?)}|*\1*|g' |
perl -pe 's|<<|```{r |g' |
perl -pe 's|>>=|}|g' |

mikelove

library(BSgenome.Hsapiens.UCSC.hg38)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
txs <- extractTranscriptSeqs(Hsapiens, TxDb.Hsapiens.UCSC.hg38.knownGene)
z <- txs[sample(length(txs), 10000)]
z <- z[width(z) > 100]
starts <- round(runif(length(z),1,width(z)-99))
gc <- as.vector(letterFrequency(subseq(z,start=starts,width=100),"GC"))
with(hist(gc), plot(mids, density, type="b", lwd=2))
abline(h=0)

mikelove

get_deps <- function(what="Suggests") {
  deps <- desc::desc_get_deps()
  suggests <- deps$package[deps$type==what]
  setdiff(suggests, sub(".*/","",find.package(suggests, quiet=TRUE)))
}

mikelove

# suspend, foreground, background

Ctrl-z, fg, jobs, bg

example in R: sapply(1:100, function(i) {Sys.sleep(1);print(i)})

# list size of directories

du -sh *

mikelove

---
title: "Using RNA-seq DE methods to detect allele-specific expression"
author: "Michael Love"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: html_document
---

The question has come up a few times on the Bioconductor support site how to use
methods like DESeq2 or edgeR to detect allele-specific expression, 
and how to see if the allelic ratio differs across condition. Aaron Lun has written up 

mikelove

library(rvest)

org <- "Takifugu_rubripes"

getdetails <- function(org) {
  readit <- function(org, prefix) {
    read_html(paste0("http://",prefix,".ensembl.org/",
                     org, "/Info/Annotation"))
  }
  page <- tryCatch(readit(org, "www"),