dfjenkins3

# Comparing GenTox with Bacterial.Mutagenesis

```{r}
library(Biobase)

setwd(file.path("C:","Users","djenk","OneDrive","grad_school","05-2015_fall",
                "BS830_microarray","20151218-Final_Project"))

#TG-GATEs Data (Discovery Set)
load("Rat.Liver.in_vivo.repeat.annotated.RData")

dfjenkins3

# Comparing GenTox with Bacterial.Mutagenesis

```{r}
library(Biobase)

setwd(file.path("C:","Users","djenk","OneDrive","grad_school","05-2015_fall",
                "BS830_microarray","20151218-Final_Project"))

#TG-GATEs Data (Discovery Set)
load("Rat.Liver.in_vivo.repeat.annotated.RData")

dfjenkins3

#install reference batch from github
library(devtools)
install_github("wevanjohnson/sva-devel", ref="reference_batch")
library(sva)

#example ComBat call with reference batch
combat<-ComBat(dat=indata, batch=c(rep(1,100),rep(2,100)), mod=NULL, ref.batch=2)

dfjenkins3

setwd("C:/Users/dfj/Desktop/")

data("trainingData1")
data("testData1")
data("geneList1")

trainingLabel1 <- list(control = list(bcat=1:10), bcat = 11:19)
testLabel1 <- rep(c("subtypeA","subtypeB"),c(53,58))

tempdir <- "delta_test9"

dfjenkins3

library("devtools")
install_github("dfjenkins3/ASSIGN")
library("ASSIGN")
data(trainingData1)
data(testData1)
data(geneList1)
tempdir <- "test2"
trainingLabel1 <- list(control = list(bcat=1:10, e2f3=1:10,
                       myc=1:10, ras=1:10, src=1:10),
                       bcat = 11:19, e2f3 = 20:28, myc= 29:38,

dfjenkins3

IGV Batch Screenshots

IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.

Table of Contents

1. Requirements
2. Workflow
3. Create BED File

dfjenkins3

wget http://downloads.sourceforge.net/project/flashpage/FLASH-1.2.11.tar.gz
tar -xvf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11
make
./flash

dfjenkins3

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Std;

####################################################################################
# vcfsorter.pl
#
# Copyright (C) 2011 German Gaston Leparc
#

dfjenkins3

Chromosome 21 Subset, no filter applied

Run	chr21 subset	chr21 subset	chr21 subset
Exclude	none	lcr	speedseq
Filter	all	all	all
Deletions	212	186	116
Duplications	43	36	11
Interchroms	5	5	0
Inversions	10	9	7

dfjenkins3

chr21 subset lumpy results:

>cat 3_2014-05-06_ceu-sort-svs-NA12878-filter.bedpe | awk '$1=='21' || $4=='21'' | cut -f11 | sort | uniq -c
    212 TYPE:DELETION
     43 TYPE:DUPLICATION
      5 TYPE:INTERCHROM
     10 TYPE:INVERSION