grimbough

library(ShortRead)

## create a single string with the number of characters defined by 'length'
## and the letter sampled from 'alphabet'
generateString <- function(length = 50, alphabet = c("A","C","G","T") ) { 
    paste0(sample(alphabet, size = length, replace = TRUE), collapse = "") 
}

## create a ShortReadQ object containing 'nreads' reads, each of which has length 'length'
createFastq <- function(nreads, length) {

grimbough

fullXmlQuery <- "<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE Query>
        <Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'>
            <Dataset name = 'hsapiens_gene_ensembl'>
                <Attribute name = 'ensembl_transcript_id'/>
                <Attribute name = 'ensembl_exon_id'/>
                <Attribute name = 'rank'/>
                <Attribute name = 'genomic_coding_start'/>
                <Attribute name = 'cds_start'/>
                <Attribute name = '5_utr_start'/>
            </Dataset>

grimbough

    fullXmlQuery <- "<?xml version='1.0' encoding='UTF-8'?> <!DOCTYPE Query>
        <Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'>
            <Dataset name = 'hsapiens_gene_ensembl'>
                <Attribute name = 'phenotype_description'/>
                <Attribute name = 'ensembl_gene_id'/>
                <Filter name = 'ensembl_gene_id' value = 'ENSG00000094804'/>
            </Dataset>
        </Query>"

    rcurl_return <- RCurl::postForm(uri = "http://www.ensembl.org:80/biomart/martservice?", 

grimbough

library(TENxBrainData)
library(ggplot2)
library(tidyr)

tenx <- TENxBrainData()

ncols <- c(1,2,5,10,20,50,100,200,500,1000)

svd <- bda <- numeric(length = length(ncols))

grimbough

library(ggplot2)
library(gridExtra)

## create 17 plots, where the only element is a number in the centre
res <- list()
for(i in 1:17) {
    x <- data.frame(x = 1, y = 1, num = as.character(i))
    res[[i]] <- ggplot(x, aes(x = x, y = y, label = num)) + 
        geom_text() +
        theme_void() +

grimbough

library(rhdf5)

hslab_bm <- function(m = 10000, n = 10000) {
    ## TENxBrainData
    fid <- H5Fopen('/media/Storage/Work/ExperimentHub/1040')
    did <- H5Dopen(h5loc = fid, 'counts')
    sid <- H5Dget_space(did)

    ## select first 100 rows and a random (ordered) sample of columns
    index <- list(1:100,

grimbough

WD <- tempdir()
setwd(WD)
library(EBImage)
library(tidyverse)

## download example zip file ad unpack
download.file('https://www.dropbox.com/s/40e5tfohgdm9wlo/IF015_plate002_test.zip?dl=1',
              destfile = 'IF015_plate002.zip', mode = "wb")
unzip('IF015_plate002.zip')

grimbough

BiocManager::install("grimbough/rhdf5", ref = "f06ab6f",
                     update = FALSE, ask = TRUE, INSTALL_opts = c('--no-lock'))

suppressPackageStartupMessages(library(rhdf5))
suppressPackageStartupMessages(library(microbenchmark))
suppressPackageStartupMessages(library(ggplot2))
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(stringr))

h5file <- "/tmpdata/msmith/ExperimentHub/2230"

grimbough

This code chunk will extract all code blocks from `example.Rmd` and write them to a temporary file, preservining chunk options. It will then read them and make those chunks avaliable in the current R environment when the presentation is knitted.

```{r include, eval=TRUE, echo=FALSE, include = FALSE}
tmp_script <- tempfile()
knitr::purl("example.Rmd", output=tmp_script, quiet = TRUE)
knitr::read_chunk(tmp_script)
```

We can then include a chunk from `example.Rmd` like so:

grimbough

/*
 *  Confirming hyperslab issue remains when combining two selections 
 *  using H5Scombine_select
 */

#include <hdf5.h>
#include <stdlib.h>

#define FILE        "subset.h5"
#define DATASETNAME "IntArray"