Last updated: 2018-07-19

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    File Version Author Date Message
    Rmd 0d7956a Briana Mittleman 2018-07-19 add smash analysis

Use SMASH to smooth regions of the Netseq data.

I want to use the first 8 lines (NET3)

  • 18505

  • 18508

  • 18486

  • 19239

  • 19141

  • 19193

  • 19257

  • 19128

The coverage files I need to make the matrix are in /project2/gilad/briana/Net-seq-pilot/data/cov.

ACTB

I am going to look at the region chr7:5,565,291-5,573,483 around the actb gene.

#!/bin/bash

#SBATCH --job-name=testsmash.actb
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=testsmash.actb.out
#SBATCH --error=testsmash.actb.err
#SBATCH --partition=broadwl
#SBATCH --mem=20G
#SBATCH --mail-type=END

awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-18486_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-18486_combined_Netpilot-actb.bed



awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-18505_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-18505_combined_Netpilot-actb.bed

awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-18508_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-18508_combined_Netpilot-actb.bed



awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19128_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19128_combined_Netpilot-sort.actb.bed


awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19141_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19141_combined_Netpilot.actb.bed


awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19193_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19193_combined_Netpilot.actb.bed


awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19239_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19239_combined_Netpilot.actb.bed


awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19257_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19257_combined_Netpilot.actb.bed

Load Packages:

library(devtools)
Warning: package 'devtools' was built under R version 3.4.4
library(scales)
library(smashr)
library(tidyr)
library(workflowr)
Loading required package: rmarkdown
This is workflowr version 1.0.1
Run ?workflowr for help getting started
library(dplyr)
Warning: package 'dplyr' was built under R version 3.4.4

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
actb_18486=read.table("../data/smash_test/YG-SP-NET3-18486_combined_Netpilot-actb.bed", col.names=c("chr", "base", "net18486"))

actb_18505=read.table("../data/smash_test/YG-SP-NET3-18505_combined_Netpilot-actb.bed", col.names=c("chr", "base", "net18505"))

actb_18508=read.table("../data/smash_test/YG-SP-NET3-18508_combined_Netpilot-actb.bed", col.names=c("chr", "base", "net18508"))

actb_19128=read.table("../data/smash_test/YG-SP-NET3-19128_combined_Netpilot.actb.bed", col.names=c("chr", "base", "net19128"))

actb_19141=read.table("../data/smash_test/YG-SP-NET3-19141_combined_Netpilot.actb.bed", col.names=c("chr", "base", "net19141"))

actb_19193=read.table("../data/smash_test/YG-SP-NET3-19193_combined_Netpilot.actb.bed", col.names=c("chr", "base", "net19193"))

actb_19239=read.table("../data/smash_test/YG-SP-NET3-19239_combined_Netpilot.actb.bed", col.names=c("chr", "base", "net19239"))

actb_19257=read.table("../data/smash_test/YG-SP-NET3-19257_combined_Netpilot.actb.bed", col.names=c("chr", "base", "net19257"))

Make matrix

actb_matrix=cbind(actb_18486$net18486, actb_18505$net18505,actb_18508$net18508, actb_19128$net19128, actb_19141$net19141,actb_19193$net19193, actb_19239$net19239, actb_19257$net19257) %>%t

write the matrix out:

#write.table(actb_matrix, "../data/smash_test/actb_countmatrix.txt", quote = F, row.names = F, col.names = F)

Run smash:

actb_res = smash.poiss(actb_matrix[1,]+actb_matrix[2,]+ actb_matrix[3,]+ actb_matrix[4,]+actb_matrix[5,]+actb_matrix[6,]+actb_matrix[7,]+actb_matrix[8,], post.var=TRUE)
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region=5565291:5573483


plot(region,actb_res$est,type='l',xlab="position",ylab="intensity", main="SMASH results ACTB")

Next I want to run it seperatly for all 8 individuals and plot them together to see if the peaks line up.

actb_res1 = smash.poiss(actb_matrix[1,], post.var=TRUE)
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actb_res2 = smash.poiss(actb_matrix[2,], post.var=TRUE)
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actb_res3 = smash.poiss(actb_matrix[3,], post.var=TRUE)
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actb_res4 = smash.poiss(actb_matrix[4,], post.var=TRUE)
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
actb_res5 = smash.poiss(actb_matrix[5,], post.var=TRUE)
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
actb_res6 = smash.poiss(actb_matrix[6,], post.var=TRUE)
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
actb_res7 = smash.poiss(actb_matrix[7,], post.var=TRUE)
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
actb_res8 = smash.poiss(actb_matrix[8,], post.var=TRUE)
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm
Due to absence of package REBayes, switching to EM algorithm

Make results matrix:

res_matrix=rbind(actb_res$est,actb_res1$est,actb_res2$est,actb_res3$est,actb_res4$est,actb_res5$est,actb_res6$est,actb_res7$est,actb_res8$est)

#write.table(res_matrix, "../data/smash_test/actb_smash_res.txt", quote = F, col.names = F, row.names = F, sep="\t")
par(mfrow=c(3,3))
plot(region,actb_res$est,type='l',xlab="position",ylab="intensity", main="Combined")
plot(region,actb_res1$est,type='l',xlab="position",ylab="intensity", main="18486")
plot(region,actb_res2$est,type='l',xlab="position",ylab="intensity",main="18505")
plot(region,actb_res3$est,type='l',xlab="position",ylab="intensity",main="18508")
plot(region,actb_res4$est,type='l',xlab="position",ylab="intensity",main="19128")
plot(region,actb_res5$est,type='l',xlab="position",ylab="intensity",main="19141")
plot(region,actb_res6$est,type='l',xlab="position",ylab="intensity",main="19193")
plot(region,actb_res7$est,type='l',xlab="position",ylab="intensity",main="19239")
plot(region,actb_res8$est,type='l',xlab="position",ylab="intensity",main="19257")

I also am going to run it on the Mayer hek data.

#!/bin/bash

#SBATCH --job-name=testsmash.actb
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=testsmash.actb.out
#SBATCH --error=testsmash.actb.err
#SBATCH --partition=broadwl
#SBATCH --mem=20G
#SBATCH --mail-type=END


awk '$1 == 7 && $2 >= 5565291 && $2 <= 5573483 {print}' /project2/gilad/briana/mayer.data/mayer_hek/data/cov/mayer_hek-sort.dedup.cov.bed > /project2/gilad/briana/mayer.data/mayer_hek/data/mayer_hek-dedup-smashactb.bed

This is not the correct coverage file to run this on. I need to make a genome coverage file of the data then I can run this.

COMT

Second gene to look at COMT chr22:19,928,209-19,960,444

#!/bin/bash

#SBATCH --job-name=testsmash.comt
#SBATCH --account=pi-yangili1
#SBATCH --time=24:00:00
#SBATCH --output=testsmash.comt.out
#SBATCH --error=testsmash.comt.err
#SBATCH --partition=broadwl
#SBATCH --mem=20G
#SBATCH --mail-type=END

awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-18486_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-18486_combined_Netpilot-comt.bed



awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-18505_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-18505_combined_Netpilot-comt.bed

awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-18508_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-18508_combined_Netpilot-comt.bed



awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19128_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19128_combined_Netpilot-sort.comt.bed


awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19141_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19141_combined_Netpilot.comt.bed


awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19193_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19193_combined_Netpilot.comt.bed


awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19239_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19239_combined_Netpilot.comt.bed


awk '$1 == 22 && $2 >= 19928209 && $2 <= 19960444 {print}' /project2/gilad/briana/Net-seq-pilot/data/cov/YG-SP-NET3-19257_combined_Netpilot-sort.cov.bed > /project2/gilad/briana/Net-seq-pilot/data/smash.test/YG-SP-NET3-19257_combined_Netpilot.comt.bed

Session information

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_0.7.5     workflowr_1.0.1 rmarkdown_1.8.5 tidyr_0.7.2    
[5] smashr_1.2-0    scales_0.5.0    devtools_1.13.6

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17      bindr_0.1.1       pillar_1.1.0     
 [4] compiler_3.4.2    git2r_0.21.0      plyr_1.8.4       
 [7] R.methodsS3_1.7.1 R.utils_2.6.0     bitops_1.0-6     
[10] iterators_1.0.10  tools_3.4.2       digest_0.6.15    
[13] tibble_1.4.2      evaluate_0.10.1   memoise_1.1.0    
[16] lattice_0.20-35   pkgconfig_2.0.1   rlang_0.2.1      
[19] Matrix_1.2-12     foreach_1.4.4     yaml_2.1.19      
[22] parallel_3.4.2    bindrcpp_0.2.2    withr_2.1.1      
[25] stringr_1.3.1     knitr_1.18        caTools_1.17.1   
[28] tidyselect_0.2.4  rprojroot_1.3-2   grid_3.4.2       
[31] glue_1.2.0        data.table_1.11.4 R6_2.2.2         
[34] purrr_0.2.5       ashr_2.2-7        magrittr_1.5     
[37] whisker_0.3-2     backports_1.1.2   codetools_0.2-15 
[40] htmltools_0.3.6   MASS_7.3-48       assertthat_0.2.0 
[43] colorspace_1.3-2  wavethresh_4.6.8  stringi_1.2.2    
[46] munsell_0.4.3     doParallel_1.0.11 pscl_1.5.2       
[49] truncnorm_1.0-8   SQUAREM_2017.10-1 R.oo_1.22.0

This reproducible R Markdown analysis was created with workflowr 1.0.1