kippjohnson

Keybase proof

I hereby claim:

• I am kippjohnson on github.
• I am kippp (https://keybase.io/kippp) on keybase.
• I have a public key ASBBGwy60nktkTN-Q5zxTA9io6vTJdT4eNXWIwtzWp-pBgo

To claim this, I am signing this object:

kippjohnson

{"nodes":[{"name":" Andrew Kasarskis","ntimes":7,"id":" Andrew Kasarskis"},{"name":" Atul J Butte","ntimes":8,"id":" Atul J Butte"},{"name":" Ben Readhead","ntimes":12,"id":" Ben Readhead"},{"name":" Bin Chen","ntimes":5,"id":" Bin Chen"},{"name":" Brian A Kidd","ntimes":4,"id":" Brian A Kidd"},{"name":" Eric E Schadt","ntimes":6,"id":" Eric E Schadt"},{"name":" Jagat Narula","ntimes":5,"id":" Jagat Narula"},{"name":" Khader Shameer","ntimes":18,"id":" Khader Shameer"},{"name":" Li Li","ntimes":18,"id":" Li Li"},{"name":" Marcus A Badgeley","ntimes":6,"id":" Marcus A Badgeley"},{"name":" Max S Tomlinson","ntimes":4,"id":" Max S Tomlinson"},{"name":" Riccardo Miotto","ntimes":5,"id":" Riccardo Miotto"},{"name":" Rong Chen","ntimes":13,"id":" Rong Chen"},{"name":" Samin K Sharma","ntimes":4,"id":" Samin K Sharma"},{"name":" Shameer Khader","ntimes":4,"id":" Shameer Khader"},{"name":" Yuliya Vengrenyuk","ntimes":6,"id":" Yuliya Vengrenyuk"},{"name":"Beau Norgeot","ntimes":4,"id":"Beau Norgeot"},{"name":"Benjamin

kippjohnson

FROM rocker/rstudio:3.6.1

RUN apt-get update -qq && apt-get -y --no-install-recommends install \
  libxml2-dev \
  libcairo2-dev \
  libsqlite3-dev \
  libmariadbd-dev \
  libmariadb-client-lgpl-dev \
  libpq-dev \
  libssh2-1-dev \

kippjohnson

> rm(list=ls())
> set.seed(123)
> library(data.table)
> library(feather)
> library(tidyverse)
> dsize=1e7
> nc <- 100
> x <- data.frame(matrix(rnorm(dsize), ncol=nc))
> ###
> ### write.table

kippjohnson

library(data.table)
library(ggplot2)
library(ggsci)

dat <- fread("~/Downloads/neoplasm_vs_circulatory_mortality_parsed.txt")
colnames(dat) <- c("V0", "Gender", "GenderCode", "CauseOfDeath", "ICD", "Year", "Year1", "Deaths", "Population", "CrudeRate","AgeAdjustedRate")
dat$Cause <- plyr::mapvalues(dat$CauseOfDeath, from=c("Diseases of the circulatory system","Neoplasms"), to=c("Circulatory\nSystem","Neoplasm"))

ggplot(dat, aes(x=Year, y=CrudeRate, color=Gender, linetype=Cause)) + 
  geom_line() + 

kippjohnson

	"Female"	"F"	"Neoplasms"	"C00-D48"	"1999"	"1999"	270713	142237295	190.3	171.7
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2000"	"2000"	273996	143368343	191.1	171.8
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2001"	"2001"	273634	145077463	188.6	169.2
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2002"	"2002"	275266	146394634	188.0	167.7
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2003"	"2003"	275788	147679036	186.7	165.4
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2004"	"2004"	273874	148977286	183.8	162.1
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2005"	"2005"	275780	150319521	183.5	160.5
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2006"	"2006"	276957	151732647	182.5	158.6
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2007"	"2007"	276966	153166353	180.8	156.0
	"Female"	"F"	"Neoplasms"	"C00-D48"	"2008"	"2008"	277219	154604015	179.3	153.3

kippjohnson

## Concerns thought experiment in 
## Common sequence variants affect molecular function more than rare variants?
## https://www.nature.com/articles/s41598-017-01054-2.pdf
## page 8, first section of discussion
## Doesn't seem right.

rm(list=ls())
set.seed(123)

kippjohnson

## Kipp Johnson
## Ugly code to find all potential merged rsIDs
rm(list=ls())
setwd('~/Dropbox/DudleyLab/chayakrit/pad_gwas/validation/')

## packages
library(data.table)
library(httr)
library(jsonlite)