Johannes Waage jwaage
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| source("lib/check_packages.R") | |
| check_packages() | |
| load("data/ubp_phyloseq_metagenomeseq.RData") | |
| library(vegan) | |
| library(ggplot2) | |
| library(cluster) | |
| library(phyloseq) | |
| library(cowplot) | |
| library(reshape2) | |
| library(scales) |
jwaage
/ getGenotypes.R
Created
January 25, 2016 11:10
Get genotypes from SQL server (must be on COPSAC net)
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| getSNPImputed <- function(SNPs) | |
| { | |
| #Counting allele 1 | |
| if (!require("data.table")) stop("Install packages data.table") | |
| if (!require("RMySQL")) stop("Install packages RMySQL") | |
| if (!require("rio")) stop("Install packages rio") | |
| if (!require("gtools")) stop("Install packages gtools") | |
| convertProbsToDoses <- function(props, alleleToReturnAorB="A") |
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| # Welcome to the COPSAC ggplot Kaplan-Meier template. It builds nice and very customizable KM curves as shown below. Please run the two functions to load into memory, it works like a SAS macro. | |
| # Load dependencies | |
| library(survival) | |
| library(ggplot2) | |
| library(cowplot) | |
| library(reshape2) | |
| # Run these functions to load into memory | |
| # Define custom function to create a survival data.frame. Credit http://www.ceb-institute.org/bbs/wp-content/uploads/2011/09/handout_ggplot2.pdf | |
| createSurvivalFrame <- function(f.survfit){ |
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