sinarueeger

Notes from useR!2019

ToC

• Wednesday
• Thursday
• Friday

Slides + Material

• Program + Slides: https://user2019.r-project.org/talk_schedule/

sinarueeger

NCBI vs OPENSNP

• split ropensnp and ncbi functions? ¯_(ツ)_/¯
• adding a opensnp or dbsnp suffix to function name? see also https://ropensci.github.io/dev_guide/building.html#function-and-argument-naming

Function design

• what about searching for pos and chr?
• some of the functions only work for 1 SNP. extend for a vector of SNPs (e.g. genotypes())
• add progressbar

sinarueeger

## /////////////////////////////////
##       satRday Paris notes 
##            (untidy)
## /////////////////////////////////

## Lionel Henry: Programming in the tidyverse
## tidyverse (data analysis, data manipulation, data cleaning) <----> r-lib (production prgramming)
##                                       dplyr, ggplot2, tidyr <----> vctrs, rland, devtools
## reprocibillity by few users                                 <----> reusability by many users

sinarueeger

## Schur complement

sinarueeger

---
title: "icons"
output:
  pdf_document:
    toc: true
    latex_engine: pdflatex
    dev: cairo_pdf
monofont: Menlo
---

sinarueeger

library(readbitmap)
library(gganimate)
library(dplyr)
library(ggplot2)
b1 <- read.bitmap("~/Documents/rladies.png")
b2 <- read.bitmap("~/Documents/sydney.png")
x1 <- 1 - b1[,,1]
x2 <- 1 - b2[,,1]
# plot(raster::raster(x1)) # check
# plot(raster::raster(x2)) # check

sinarueeger

Here are some extra (unpolished) code snippets for the R-package `biomaRt` that came up during the writing of the [blogpost](https://sinarueeger.github.io/content/post/2018-07-27-GWAS-annotation). 

## Extract all SNPs for a particular genomic region

```{r, get-snp-info-pos-chr, include = TRUE, cache=TRUE, eval=FALSE}

library(biomaRt)

## select mart
snpmart = useMart(biomart = "ENSEMBL_MART_SNP", dataset="hsapiens_snp")

sinarueeger

Streaming, recording, webinars

Below are instructions how to get streaming, recording or webinars working.

Setup livestream

Livestreaming of a meetup is a great opportunity for people who cannot be present otherwise (e.g. other responsibilities or because they are located elsewhere). However, unless expensive technical equipment is used and lots of social media interaction happens, the quality of a livestream will not replace the actual physical meetup experience.

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Keybase proof

I hereby claim:

• I am sinarueeger on github.
• I am sinarueeger (https://keybase.io/sinarueeger) on keybase.
• I have a public key ASCtlOlKL1ZrEZvqfhqahEU4CXvSGXcV7K45RJUytntxoAo

To claim this, I am signing this object:

sinarueeger

Ressources to learn git

This is a small compilation of links to get started and familiar with git, github, command-line and R.

• Learn git with exercises and a console in a browser: try.github.io >> does not take long and is fun.

• Happy git with R is a great manual to learn git for RStudio, includes tipps and tricks and more ressources.

• SOS for git along the line oh shit, I did so and so, how can I make it right again?: ohshitgit.com.