Last updated: 2021-10-25

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Knit directory: smash-gen/

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Rmd f000105 Dongyue 2018-06-03 chip exo 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 then apply smashgen to the augmented data.

Setup

source('code/smash_gen_poisson.R')

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))
}


real_study = function(file.name,plot.name){
  
  chipexo1 <- extract_counts_CTCF(file.name)
  print(paste("proportion of 0s:", round(sum(chipexo1$counts==0)/length(chipexo1$counts),2)))

#dash.out=dash_smooth(chipexo1$counts, dash_control = list(Inf_weight = 1), progressbar = FALSE)
smash.out=smash.poiss(chipexo1$counts)
#y=reflect(chipexo1$counts,'both',c(300,299))
smashgen.vst.out=smash.gen.poiss(chipexo1$counts,smooth_method = 'smash',transformation = 'vst',robust = F)
smashgen.lik.out=smash.gen.poiss(chipexo1$counts,smooth_method = 'smash',
                                 transformation = 'lik_expansion',ash.pm = FALSE,robust = F)
fit.pois.gaus = smash.pois.gaus(chipexo1$counts)

plot(chipexo1$counts, col = "gray80", type = "p", pch=20,ylab = "counts", xlab = "", main = plot.name)
lines(smash.out, col = "blue", lwd = 1)
#lines(dash.out$estimate, col = "red", lwd = 1)
lines(smashgen.vst.out$lambda.est,col="red",lwd=2)
lines(smashgen.lik.out$lambda.est,col='black',lwd=2)

lines(fit.pois.gaus$lambda.est,col=3)
  legend("topright", # places a legend at the appropriate place
       c("data","smash-poiss",'smash-gen-vst','smash-gen-lik','smash-pois-gaus'), # puts text in the legend
       lty=c(1,1,1,1,1), # gives the legend appropriate symbols (lines)
       lwd=c(1,1,1,1,1),
       cex = 0.5,
       col=c("gray80","blue", "red",'black',3))

print(paste("nugget effect estimated by vst:",round(smashgen.vst.out$nugget.est,2)))
print(paste("nugget effect estimated by lik_expansion:",round(smashgen.lik.out$nugget.est,2)))

}

EncodeBroadHistoneHelas - Rep 1

Forward

file.name = "data/chipexo_examples/example_CTCF_MACE_wgEncodeBroadHistoneHelas3CtcfStdAlnRep1_forward_counts.txt"
real_study(file.name,plot.name = "EncodeBroadHistoneHelas - Rep 1 - forward")
[1] "proportion of 0s: 0.81"

Version Author Date
364a81a Dongyue Xie 2020-09-08
65bf7cd Dongyue Xie 2020-09-07
a1b44cb Dongyue 2018-06-03 
[1] "nugget effect estimated by vst: 0"
[1] "nugget effect estimated by lik_expansion: 1.49"

Reverse

file.name = "data/chipexo_examples/example_CTCF_MACE_wgEncodeBroadHistoneHelas3CtcfStdAlnRep1_reverse_counts.txt"

real_study(file.name,plot.name = "EncodeBroadHistoneHelas - Rep 1 - reverse")
[1] "proportion of 0s: 0.84"

Version Author Date
364a81a Dongyue Xie 2020-09-08
65bf7cd Dongyue Xie 2020-09-07
a1b44cb Dongyue 2018-06-03 
[1] "nugget effect estimated by vst: 0"
[1] "nugget effect estimated by lik_expansion: 0"

EncodeOpenChromChipHelas - Rep 1

Forward

file.name = "data/chipexo_examples/example_CTCF_MACE_wgEncodeOpenChromChipHelas3CtcfAlnRep1_forward_counts.txt"


real_study(file.name,plot.name = "EncodeOpenChromChipHelas - Rep 1 - Forward")
[1] "proportion of 0s: 0.83"

Version Author Date
364a81a Dongyue Xie 2020-09-08
65bf7cd Dongyue Xie 2020-09-07
a1b44cb Dongyue 2018-06-03 
[1] "nugget effect estimated by vst: 0"
[1] "nugget effect estimated by lik_expansion: 0.8"

Reverse

file.name = "data/chipexo_examples/example_CTCF_MACE_wgEncodeOpenChromChipHelas3CtcfAlnRep1_reverse_counts.txt"

real_study(file.name,plot.name = "EncodeOpenChromChipHelas - Rep 1 - reverse")
[1] "proportion of 0s: 0.81"

Version Author Date
364a81a Dongyue Xie 2020-09-08
65bf7cd Dongyue Xie 2020-09-07
a1b44cb Dongyue 2018-06-03 
[1] "nugget effect estimated by vst: 0"
[1] "nugget effect estimated by lik_expansion: 0.96"

EncodeOpenChromChipHelas - Rep 2

Forward

file.name = 'data/chipexo_examples/example_CTCF_MACE_wgEncodeOpenChromChipHelas3CtcfAlnRep2_forward_counts.txt'
real_study(file.name,plot.name = "EncodeOpenChromChipHelas - Rep 2 - Forward")
[1] "proportion of 0s: 0.79"

Version Author Date
364a81a Dongyue Xie 2020-09-08
65bf7cd Dongyue Xie 2020-09-07
a1b44cb Dongyue 2018-06-03 
[1] "nugget effect estimated by vst: 0"
[1] "nugget effect estimated by lik_expansion: 0.98"

Reverse

file.name = "data/chipexo_examples/example_CTCF_MACE_wgEncodeOpenChromChipHelas3CtcfAlnRep2_reverse_counts.txt"
real_study(file.name,plot.name = "EncodeOpenChromChipHelas - Rep 2 - reverse")
[1] "proportion of 0s: 0.78"

Version Author Date
364a81a Dongyue Xie 2020-09-08
65bf7cd Dongyue Xie 2020-09-07
a1b44cb Dongyue 2018-06-03 
[1] "nugget effect estimated by vst: 0"
[1] "nugget effect estimated by lik_expansion: 0.83"

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ashr_2.2-50      wavethresh_4.6.8 MASS_7.3-51.4    smashr_1.2-9    
[5] workflowr_1.6.2 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5        knitr_1.23        whisker_0.3-2    
 [4] magrittr_1.5      SQUAREM_2017.10-1 lattice_0.20-38  
 [7] R6_2.4.0          stringr_1.4.0     caTools_1.17.1.2 
[10] tools_3.6.1       grid_3.6.1        data.table_1.13.2
[13] xfun_0.8          irlba_2.3.3       invgamma_1.1     
[16] git2r_0.26.1      htmltools_0.3.6   yaml_2.2.0       
[19] digest_0.6.20     rprojroot_2.0.2   mixsqp_0.3-17    
[22] Matrix_1.2-18     later_0.8.0       bitops_1.0-6     
[25] promises_1.0.1    fs_1.3.1          glue_1.3.1       
[28] evaluate_0.14     rmarkdown_1.13    stringi_1.4.3    
[31] compiler_3.6.1    truncnorm_1.0-8   httpuv_1.5.1