https://divingintogeneticsandgenomics.com/tags/dplyr/ Recent content in Dplyr on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Tue, 02 Jan 2018 11:00:00 -0800 https://divingintogeneticsandgenomics.com/archive/cancer-gene-census-copy-number/ Tue, 02 Jan 2018 11:00:00 -0800 https://divingintogeneticsandgenomics.com/archive/cancer-gene-census-copy-number/ Ming Tang January 2, 2018 Set up knitr will force changing current working directory: https://philmikejones.wordpress.com/2015/05/20/set-root-directory-knitr/ https://github.com/yihui/knitr/issues/277 or use the ezkintr package https://deanattali.com/blog/ezknitr-package/ library(knitr) library(here) ## here() starts at /Users/mtang1/projects/mixing_histology_lung_cancer root.dir<- here() opts_knit$set(root.dir = root.dir) read in the data I am going to check the COSMIC database on cancer genes. Specifically, I want to know which cancer-related genes are found amplified and which are deleted. The data can be downloaded from http://cancer. https://divingintogeneticsandgenomics.com/archive/weather-and-crimes-in-chicago/ Mon, 05 Jun 2017 18:45:00 -0700 https://divingintogeneticsandgenomics.com/archive/weather-and-crimes-in-chicago/ Weather and crimes in Chicago Ming Tang June 4, 2017 How the story starts I was attending 2017 American Society of Clinical Oncology (ASCO) annual meeting in Chicago. It was my first time to do a uber from the airport to our hotel. We had a nice uber driver and we talked a lot about the city. He said he grew up in the south part of Chicago and there are a lot of crimes there. https://divingintogeneticsandgenomics.com/archive/everyone-will-write-a-blog-post-on-dplyr/ Fri, 26 Sep 2014 12:28:00 -0700 https://divingintogeneticsandgenomics.com/archive/everyone-will-write-a-blog-post-on-dplyr/ dply is a nice R package to manipulate big data. There are several good tutorials I came across: http://www.dataschool.io/dplyr-tutorial-for-faster-data-manipulation-in-r/ http://stat545-ubc.github.io/block009_dplyr-intro.html http://stat545-ubc.github.io/bit001_dplyr-cheatsheet.html http://gettinggeneticsdone.blogspot.com/2014/08/do-your-data-janitor-work-like-boss.html I followed the example in the early edition of Bioinformatics Data Skills on the dplyr part and put a gist below. The example used dplyr to manipulate and summarize the human annotation gff file downloaded here http://useast.ensembl.org/info/data/ftp/index.html. I downloaded the ensemble 74 build which is different from the 75 build in the example of the book.