R

It is almost the end of 2018. It is a good time to review what I have achieved during the year and look forward to a brand new 2019. I wrote a similar post for 2017 here. Some highlights of the year 2018: My son Noah Tang was born in April. He is so lovely and we love him so much. Can’t believe he is almost 9 months old.

During my daily work with R for genomic data analysis, I encountered several instances that R gives me some (bad) surprises. 1. The devil 1 and 0 coordinate system read detail here https://github.com/crazyhottommy/DNA-seq-analysis#tips-and-lessons-learned-during-my-dna-seq-data-analysis-journey some files such as bed file is 0 based. Two genomic regions: chr1 0 1000 chr1 1001 2000 when you import that bed file into R using rtracklayer::import(), it will become chr1 1 1000 chr1 1002 2000 The function convert it to 1 based internally (R is 1 based unlike python).

Googling is a required technique for programmers. Once I have a programming problem in mind, the first thing I do is to google to see if other people have encountered the same problem and maybe they already have a solution. Do not re-invent the wheels. Actually, reading other people’s code and mimicing their code is a great way of learning. Today, I am going to show you how to compute binned averages/sums along a genome or any genomic regions of interest.

I have used blogdown writing regular markdown posts, but the real power is from the Rmarkdown! let me try it for this post. Note that you do not knit the Rmarkdown by yourself, rather you let blogdown do the heavy lift. library(tidyverse) library(ggplot2) head(mtcars) ## mpg cyl disp hp drat wt qsec vs am gear carb ## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 ## Mazda RX4 Wag 21.

I have been following this tutorial from Alison and tips from Leslie Myint for some customization for deploying my blogdown website It is quite straightforward to have a working site following Alison’s guide. However, you always want some customization of your own site. I took the tips from Leslie. changed the menue bar to black. I like it better than the default white. in the config.toml file, change the theme: