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<!DOCTYPE html> | |
<html lang="en"> | |
<head> | |
<meta charset="UTF-8"> | |
<title>Title</title> | |
<style> | |
.box { | |
height: 100px; | |
width: 100px; | |
top: 100px; |
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stat_smooth_func <- function(mapping = NULL, data = NULL, | |
geom = "smooth", position = "identity", | |
..., | |
method = "auto", | |
formula = y ~ x, | |
se = TRUE, | |
n = 80, | |
span = 0.75, | |
fullrange = FALSE, | |
level = 0.95, |
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wget http://www.openbioinformatics.org/annovar/download/annovar.latest.tar.gz.mirror | |
tar xzvf annovar.tar.gz | |
cd annovar | |
# download databases (goes to UCSC) | |
./annotate_variation.pl -buildver hg19 -downdb 1000g2010nov humandb | |
./annotate_variation.pl -buildver hg19 -downdb avsift humandb | |
./annotate_variation.pl -buildver hg19 -downdb refGene humandb | |
./annotate_variation.pl -buildver hg19 -downdb mce46way humandb/ | |
./annotate_variation.pl -buildver hg19 -downdb snp131 humandb/ |
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# .bashrc | |
# Source global definitions | |
if [ -f /etc/bashrc ]; then | |
. /etc/bashrc | |
fi | |
# User specific aliases and functions | |
### autocorrects cd misspellings, 'cd /sur/src/linus' >> 'cd /usr/src/linux' ### |
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plotPCAWithSampleNames = function(x, intgroup="condition", ntop=500) | |
{ | |
library(RColorBrewer) | |
library(genefilter) | |
library(lattice) | |
# pca | |
rv = rowVars(assay(x)) | |
select = order(rv, decreasing=TRUE)[seq_len(min(ntop, length(rv)))] | |
pca = prcomp(t(assay(x)[select,])) |