Gibbsdavidl

WITH
  --
  -- we start by translating the correlations that we got to ranks,
  -- based on sorting the genes on corrByGene "DESC"
  -- this will result in the highest positive correlation getting
  -- rank #1, etc
  -- we also lightly filter the genes by excluding any with near-zero
  -- or negative correlation coefficients, and the result is a list
  -- of approx 9000 genes with symbol, correlation, and rank
  geneScoresT AS (

Gibbsdavidl

WITH
  mutatedSamples AS (
  SELECT
    project_short_name,
    sample_barcode_tumor
  FROM
    `isb-cgc.TCGA_hg19_data_v0.Somatic_Mutation_MC3`
  WHERE
    Hugo_Symbol = 'EGFR'
    AND Variant_Type = 'SNP'

Gibbsdavidl

SELECT
 project_short_name,
  STDDEV_SAMP( protein_expression ) / AVG( protein_expression ) AS CoV
FROM
  [isb-cgc:TCGA_hg19_data_v0.Protein_Expression]
group by
 project_short_name 
order by
 CoV DESC

Gibbsdavidl

CREATE TEMP FUNCTION
  bq_linear(x ARRAY<FLOAT64>, y ARRAY<FLOAT64>)
  RETURNS FLOAT64
  LANGUAGE js AS """
    // http://tom-alexander.github.io/regression-js/

    var data = [];
    // Our data list is list of lists. The small list being each (x,y) point
    for (var i = 0; i < x.length; i++) {
      data.push([x[i],y[i]])

Gibbsdavidl

# This shows the contents of my global.R file, that contains the BigQuery SQL, googleAuthR code, and plots.


# global.R

#http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
  library(grid)
  
  # Make a list from the ... arguments and plotlist

Gibbsdavidl

/*M///////////////////////////////////////////////////////////////////////////////////////
//
//  IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
//  By downloading, copying, installing or using the software you agree to this license.
//  If you do not agree to this license, do not download, install,
//  copy or use the software.
//
//
//                          License Agreement

Gibbsdavidl

WITH
  --
  --
  --
  geneList AS (
  SELECT
    a.entrez AS Entrez,
    Symbol AS HGNC_gene_symbol
  FROM
    `isb-cgc.QotM.Reactome_a1` a

Gibbsdavidl

#!/bin/bash

# Made a tiny change to allow me to run it on Mac OS 10.11.6 #

# This script sets SSH tunnel and opens Chrome Browser with SOCKS proxy
# configured for direct access to the Jupyter cluster.

set -euo pipefail

DIR="${BASH_SOURCE%/*}"

Gibbsdavidl