adiamb

#!/usr/bin/Rscript --vanilla

###########################################################
##                                                       ##
##   elastic.R                                           ##
##                                                       ##
##                Author: Tony Fischetti                 ##
##                        tony.fischetti@gmail.com       ##
##                                                       ##
###########################################################

adiamb

## ------------------------- ##
## An Example of ##
## Automating Plot Output ##
## ------------------------- ##

names = LETTERS[1:26] ## Gives a sequence of the letters of the alphabet

beta1 = rnorm(26, 5, 2) ## A vector of slopes (one for each letter)
beta0 = 10 ## A common intercept

adiamb

#!/bin/bash

#PBS -N sleepgwas
#PBS -o sleepsnptest-output
#PBS -e sleepsnptest-error
#PBS -t 1-22
#PBS -l walltime=24:00:00
#PBS -l nodes=1:ppn=2
#PBS -S /bin/bash

adiamb

###PYTHON#############
#Purpose : Replication of MS spectra analysis
#Author : Aditya Ambati 
#date : May 14 2017
#update : version 1
#####import libraries


from itertools import chain
import pandas as pd

adiamb

import glob
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import re
def cleanimpute(x, y, z):
	cleaned_info = x[(x['info'] >= 0.8) & (x['certainty'] >= 0.8)]#x[x['certainty'] >= 0.9]
	cleaned_impute = y[y[1].isin(cleaned_info.rs_id)]
	cleaned_impute.to_csv(z, index=False, header=None)

adiamb

###PYTHON#############
#Purpose : to test Recurrent neural networks
#Author : Aditya Ambati 
#date : May 3 2017
#update : version 1
#####import libraries
import pandas as pd
import numpy as np
from sklearn.metrics import mean_squared_error
from math import sqrt

adiamb

###PYTHON#############
#Purpose : Replication of MS spectra analysis
#Author : Aditya Ambati 
#date : May 14 2017
#update : version 1
#####import libraries


from itertools import chain
import pandas as pd

adiamb

!/bin/sh
#
# set the name of the job
#$ -N hcrt_AA
#
# set the maximum memory usage (per slot)
#$ -l h_vmem=2G
#
# set the maximum run time

adiamb

Wed 15 Feb 2017 04:06:05 PM PST 
#!/bin/sh
for i in `seq 1 22`
do
command=`echo snptest -data /srv/gsfs0/projects/mignot/hcrtgwas/CHR"$i".Plate86to87.impute2 /srv/gsfs0/projects/mignot/hcrtgwas/CHR"$i".86to87.updated.sample -method score -cov_names C1 C2 C3 C4 C5 C6 C7 C8 C9 -frequentist 1 -pheno HCRT -o hcrt.plate86to87updated.CHR"$i" -exclude_samples /srv/gsfs0/projects/mignot/hcrtgwas/CHR"$i".86to87.exclusion.sample`
touch tmpchr SNPtest.$i.sh
chmod 755 SNPtest.$i.sh
echo \#\!/bin/bash >SNPtest.$i.sh
echo \#$ -N chr"$i"_SNPtest >>SNPtest.$i.sh
echo \#$ -l h_vmem=5G >>SNPtest.$i.sh

adiamb

require(data.table)
require(MatrixEQTL)
require(readr)
totalEM_DOS = as.matrix(totalEM_DOS[-c(1:3, 358)])
rownames(totalEM_DOS) = totalEM_DOS_SNP_POS$SNP
snps = SlicedData$new()
snps$CreateFromMatrix(totalEM_DOS)

maf.list = vector('list', length(snps))
for(sl in 1:length(snps)) {