stephenturner

# Function to extract the overall ANOVA p-value out of a linear model object
lmp <- function (modelobject) {
	if (class(modelobject) != "lm") stop("Not an object of class 'lm' ")
	f <- summary(modelobject)$fstatistic
	p <- pf(f[1],f[2],f[3],lower.tail=F)
	attributes(p) <- NULL
	return(p)
}

# simulate some data

stephenturner

## RNA-seq analysis with DESeq2
## Stephen Turner, @genetics_blog

# RNA-seq data from GSE52202
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl")

# Import & pre-process ----------------------------------------------------

# Import data from featureCounts

stephenturner

// Place your key bindings in this file to overwrite the defaults
[
    // RStudio: Copy lines up/down with alt+cmd+up/down
    {
        "key": "alt+cmd+down",
        "command": "editor.action.copyLinesDownAction",
        "when": "editorTextFocus && !editorReadonly"
    },
    {
        "key": "shift+alt+down",

stephenturner

stephenturner

# To source this file into an environment to avoid cluttering the global workspace, put this in Rprofile:
# my.env <- new.env(); sys.source("C:/PathTo/THIS_FILE.r", my.env); attach(my.env)

#-----------------------------------------------------------------------
#     Load packages, set options and cwd, set up database connection
#-----------------------------------------------------------------------

## Load packages
# require(ggplot2)  #plotting
# require(plyr)		#data manipulation

stephenturner

# R session 1: model training and deployment ------------------------------

library(tidymodels)
library(vetiver)
library(plumber)

# Not the way you'd actually split data - for demo only
cars_train <- mtcars[1:24,]
cars_test <- mtcars[25:32,]

stephenturner

// Place your key bindings in this file to overwrite the defaults
[
    // RStudio: Copy lines up/down with alt+cmd+up/down
    {
        "key": "alt+cmd+down",
        "command": "editor.action.copyLinesDownAction",
        "when": "editorTextFocus && !editorReadonly"
    },
    {
        "key": "shift+alt+down",

stephenturner

[
    {
        "name": "Sci-Hub Lookup",
        "alias": "Sci-Hub",
        "icon": "null",
        "_urlTemplate": "https://sci-hub.tw/{z:DOI}",
        "description": "Sci-Hub full text PDF search",
        "hidden": false,
        "_urlParams": [],
        "_urlNamespaces": {

stephenturner

#!/usr/bin/env python 

# Adds allelic depth (AD)=2 to a VCF.
# Usage: bcftools view my.vcf.gz | addad.py | bcftools sort -Oz -o my.ad.vcf.gz && tabix my.ad.vcf.gz
 
import pysam

vcf_in=pysam.VariantFile("-","r")

vcf_in.header.formats.add("AD",".","Integer","Allelic depth, hard-coded as 2")

stephenturner

# Start window and pane indices at 1 instead of 0
set -g base-index 1
set -g pane-base-index 1

# Shift arrow keys to move around panes
bind -n S-Up    select-pane -U
bind -n S-Down  select-pane -D
bind -n S-Left  select-pane -L
bind -n S-Right select-pane -R