Last updated: 2018-06-03

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    Rmd 6527008 Dongyue 2018-06-03 chip seq data analysis

The lenght of sequence here is 425, which is not a power of 2 hence causing problem when using smashgen. In this real data analysis, we reflect the data both to the left and right so that it has length of 1024 then apply smashgen to the augmented data.

Setup

library(smashrgen)
library(dashr)

extract_counts_CTCF <- function(filename){
  bed_counts <- read.table(filename, header = F, stringsAsFactors = F)
  colnames(bed_counts) <- c("chr", "start", "end", "name", "width", "counts")

  counts <- strsplit(bed_counts$counts, split = ",")[[1]]
  counts[counts == "NA"] <- 0
  counts <- as.numeric(counts)

  return(counts.l = list(chr = bed_counts$chr, start = bed_counts$start, end = bed_counts$end, counts = counts))
}

CTCF raw - Rep 1

Forward

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_raw_rep1_Forward_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Reverse

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_raw_rep1_Reverse_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

CTCF raw - Rep 2

Forward

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_raw_rep2_Forward_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Reverse

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_raw_rep2_Reverse_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

CTCF raw - Rep 3

Forward

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_raw_rep3_Forward_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Reverse

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_raw_rep3_Reverse_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

CTCF - Rep 1

Forward

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_rep1_Forward_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Reverse

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_rep1_Reverse_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

CTCF - Rep 2

Forward

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_rep2_Forward_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Reverse

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_rep2_Reverse_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

CTCF - Rep 3

Forward

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_rep3_Forward_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Reverse

chipexo1 <- extract_counts_CTCF("D:/smashgen/data/chipseq_examples/example_CTCF_rep3_Reverse_counts.txt")

dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.out=smash_gen_lite(y)

plot(chipexo1$counts, col = "gray80", type = "h", ylab = "forward strand", xlab = "", main = "CTCF raw rep 1")
lines(smash.out, col = "blue", lwd = 1)
lines(dash.out$estimate, col = "red", lwd = 2)
lines(smashgen.out[301:725],col=3,lwd=3)

legend("topright", # places a legend at the appropriate place
       c("truth","dash-m", "smash-poiss",'smash-gen'), # puts text in the legend
       lty=c(1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,2,1,3),
       cex = 0.5,
       col=c("gray80","red", "blue",3))

Session information

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] dashr_0.99.0     inline_0.3.14    Rcpp_0.12.16     smashrgen_0.1.0 
[5] wavethresh_4.6.8 MASS_7.3-47      caTools_1.17.1   ashr_2.2-7      
[9] smashr_1.1-5    

loaded via a namespace (and not attached):
 [1] compiler_3.4.0       git2r_0.21.0         workflowr_1.0.1     
 [4] R.methodsS3_1.7.1    R.utils_2.6.0        bitops_1.0-6        
 [7] iterators_1.0.8      tools_3.4.0          digest_0.6.13       
[10] evaluate_0.10        lattice_0.20-35      Matrix_1.2-9        
[13] foreach_1.4.3        yaml_2.1.19          parallel_3.4.0      
[16] LaplacesDemon_16.1.0 stringr_1.3.0        knitr_1.20          
[19] REBayes_1.3          rprojroot_1.3-2      grid_3.4.0          
[22] data.table_1.10.4-3  rmarkdown_1.8        magrittr_1.5        
[25] whisker_0.3-2        backports_1.0.5      codetools_0.2-15    
[28] htmltools_0.3.5      assertthat_0.2.0     stringi_1.1.6       
[31] Rmosek_8.0.69        doParallel_1.0.11    pscl_1.4.9          
[34] truncnorm_1.0-7      SQUAREM_2017.10-1    R.oo_1.21.0

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