DNase footprint profiles using ENCODE DNase-seq data
Kaixuan Luo
7/31/2018
Last updated: 2018-08-29
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| Rmd | ed49eff | kevinlkx | 2018-08-29 | plot DNase footprint profiles of CTCF and REST using ENCODE data |
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| Rmd | bb65514 | kevinlkx | 2018-08-29 | plot DNase footprint profiles of CTCF and REST using ENCODE data |
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| Rmd | 2f894eb | kevinlkx | 2018-08-29 | plot DNase footprint profiles of CTCF and REST using ENCODE data |
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| Rmd | a233f11 | kevinlkx | 2018-08-29 | plot DNase footprint profiles of CTCF and REST using ENCODE data |
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| Rmd | f318dd5 | kevinlkx | 2018-08-29 | plot DNase footprint profiles of CTCF and REST using ENCODE data |
functions
##### Functions #####
## load and combine count matrices
load_combine_counts <- function(tf_name, pwm_name, dir_count_matrix){
cat("Loading count matrices ... \n")
counts_fwd.df <- read.table(paste0(dir_count_matrix, "/", tf_name, "/", pwm_name, "_hg19_dnase_fwdcounts.m.gz"))
counts_rev.df <- read.table(paste0(dir_count_matrix, "/", tf_name, "/", pwm_name, "_hg19_dnase_revcounts.m.gz"))
## the first 5 columns from "bwtool extract" are chr, start, end, name, and the number of data points
counts_fwd.df <- counts_fwd.df[, -c(1:5)]
counts_rev.df <- counts_rev.df[, -c(1:5)]
colnames(counts_fwd.df) <- paste0("fwd", 1:ncol(counts_fwd.df))
colnames(counts_rev.df) <- paste0("rev", 1:ncol(counts_rev.df))
counts_combined.m <- as.matrix(cbind(counts_fwd.df, counts_rev.df))
return(counts_combined.m)
}
## select candidate sites by mapability and PWM score cutoffs
select_sites <- function(sites.df, thresh_mapability=NULL, thresh_PWMscore=NULL, readstats_name=NULL){
# cat("loading sites ...\n")
cat("Select candidate sites \n")
if(!is.null(thresh_mapability) || !is.na(thresh_mapability)){
cat("Select candidate sites with mapability >=", thresh_mapability, "\n")
idx_mapability <- (sites.df[,"mapability"] >= thresh_mapability)
}else{
idx_mapability <- rep(TRUE, nrow(sites.df))
}
if(!is.null(thresh_PWMscore) || !is.na(thresh_PWMscore)){
cat("Select candidate sites with PWM score >=", thresh_PWMscore, "\n")
idx_pwm <- (sites.df[,"pwm_score"] >= thresh_PWMscore)
}else{
idx_pwm <- rep(TRUE, nrow(sites.df))
}
if(!is.null(readstats_name)){
readstats.df <- read.table(readstats_name, header = F)
## if the readstats.df contains chrY, then it means the cell type is male, then the candidate sites should contain chrY,
## otherwise, the cell type is female, then the candidate sites on chrY should be removed.
if( "chrY" %in% readstats.df[,1] ){
cat("include chrY sites \n")
idx_chr <- (sites.df[,1] != "")
}else{
cat("chrY NOT in the bam file, filter out chrY sites \n")
## remove chrY from candidate (motif) sites
idx_chr <- (sites.df[,1] != "chrY")
}
}else{
idx_chr <- rep(TRUE, nrow(sites.df))
}
idx_select <- which(idx_mapability & idx_pwm & idx_chr)
return(idx_select)
}parameters
ver_genome <- "hg19"
flank <- 100
thresh_mapability <- 0.8
thresh_PWMscore <- 10
num_top_sites <- 1000 # plot top sites
max_cuts <- 20 # Clip extreme values
dir_data <- "~/Dropbox/research/ATAC_DNase/"CTCF in GM12878 cell type
load DNase footprint data
cell_type <- "GM12878"
tf_name <- "CTCF"
pwm_name <- "CTCF_MA0139.1_1e-5"
dir_count_matrix <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/")
dir_sites_chip <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/ChIPSeq/")
filename_sites <- paste0(dir_sites_chip, "/", "chipseq_", cell_type, "_", pwm_name, "_flank", flank, "_exp1.totalcount")
sites.df <- read.table(filename_sites, header = T, comment.char = "!", stringsAsFactors = F)
sites.df <- sites.df[, c("chr", "start", "end", "site", "pwmScore", "strand", "pValue", "mapability", "ChIP_mean")]
colnames(sites.df) = c("chr", "start", "end", "name", "pwm_score", "strand", "p_value", "mapability", "ChIP")
idx_select <- select_sites(sites.df, thresh_mapability, thresh_PWMscore)Select candidate sites
Select candidate sites with mapability >= 0.8
Select candidate sites with PWM score >= 10 sites.df <- sites.df[idx_select, ]
cat("Number of sites:", nrow(sites.df), "\n")Number of sites: 54859 counts_combined.m <- load_combine_counts(tf_name, pwm_name, dir_count_matrix)Loading count matrices ... counts_combined.m <- counts_combined.m[idx_select,]
## Clip extreme values
counts_combined.m[counts_combined.m > max_cuts] <- max_cuts
cat("Dimension of", dim(counts_combined.m), "\n")Dimension of 54859 436 if(nrow(counts_combined.m) != nrow(sites.df)){
stop("Sites not matched!")
}plot footprint profiles of highest occupancy
order_selected <- order(sites.df$ChIP, decreasing = T)[1:num_top_sites]
counts_selected.m <- counts_combined.m[order_selected,]
counts_profile <- apply(counts_selected.m, 2, mean)
par(mfrow = c(1,2))
counts <- counts_profile[1:(length(counts_profile)/2)]
plot(counts, type = "l", col = "blue", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "forward strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
counts <- counts_profile[(length(counts_profile)/2+1): length(counts_profile)]
plot(counts, type = "l", col = "red", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "reverse strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
Expand here to see past versions of unnamed-chunk-4-1.png:
| Version | Author | Date |
|---|---|---|
| 35c5feb | kevinlkx | 2018-08-29 |
## save counts matrix
rds_name <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/", tf_name, "/",
pwm_name, "_", cell_type, "_hg19_dnase_counts_selected_sites.rds")
saveRDS(counts_selected.m, rds_name)plot footprint profiles of most accessible sites
order_selected <- order(rowSums(counts_combined.m), decreasing = T)[1:num_top_sites]
counts_selected.m <- counts_combined.m[order_selected,]
counts_profile <- apply(counts_selected.m, 2, mean)
par(mfrow = c(1,2))
counts <- counts_profile[1:(length(counts_profile)/2)]
plot(counts, type = "l", col = "blue", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "forward strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
counts <- counts_profile[(length(counts_profile)/2+1): length(counts_profile)]
plot(counts, type = "l", col = "red", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "reverse strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
Expand here to see past versions of unnamed-chunk-5-1.png:
| Version | Author | Date |
|---|---|---|
| 35c5feb | kevinlkx | 2018-08-29 |
CTCF in K562 cell type
load DNase footprint data
cell_type <- "K562"
tf_name <- "CTCF"
pwm_name <- "CTCF_MA0139.1_1e-5"
dir_count_matrix <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/")
dir_sites_chip <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/ChIPSeq/")
filename_sites <- paste0(dir_sites_chip, "/", "chipseq_", cell_type, "_", pwm_name, "_flank", flank, "_exp1.totalcount")
sites.df <- read.table(filename_sites, header = T, comment.char = "!", stringsAsFactors = F)
sites.df <- sites.df[, c("chr", "start", "end", "site", "pwmScore", "strand", "pValue", "mapability", "ChIP_mean")]
colnames(sites.df) = c("chr", "start", "end", "name", "pwm_score", "strand", "p_value", "mapability", "ChIP")
idx_select <- select_sites(sites.df, thresh_mapability, thresh_PWMscore)Select candidate sites
Select candidate sites with mapability >= 0.8
Select candidate sites with PWM score >= 10 sites.df <- sites.df[idx_select, ]
cat("Number of sites:", nrow(sites.df), "\n")Number of sites: 54859 counts_combined.m <- load_combine_counts(tf_name, pwm_name, dir_count_matrix)Loading count matrices ... counts_combined.m <- counts_combined.m[idx_select,]
## Clip extreme values
counts_combined.m[counts_combined.m > max_cuts] <- max_cuts
cat("Dimension of", dim(counts_combined.m), "\n")Dimension of 54859 436 if(nrow(counts_combined.m) != nrow(sites.df)){
stop("Sites not matched!")
}plot footprint profiles of highest occupancy sites
order_selected <- order(sites.df$ChIP, decreasing = T)[1:num_top_sites]
counts_selected.m <- counts_combined.m[order_selected,]
counts_profile <- apply(counts_selected.m, 2, mean)
par(mfrow = c(1,2))
counts <- counts_profile[1:(length(counts_profile)/2)]
plot(counts, type = "l", col = "blue", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "forward strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
counts <- counts_profile[(length(counts_profile)/2+1): length(counts_profile)]
plot(counts, type = "l", col = "red", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "reverse strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
Expand here to see past versions of unnamed-chunk-7-1.png:
| Version | Author | Date |
|---|---|---|
| 35c5feb | kevinlkx | 2018-08-29 |
## save counts matrix
rds_name <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/", tf_name, "/",
pwm_name, "_", cell_type, "_hg19_dnase_counts_selected_sites.rds")
saveRDS(counts_selected.m, rds_name)REST in GM12878 cell type
load DNase footprint data
cell_type <- "GM12878"
tf_name <- "REST"
pwm_name <- "REST_MA0138.2_1e-5"
dir_count_matrix <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/")
dir_sites_chip <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/ChIPSeq/")
filename_sites <- paste0(dir_sites_chip, "/", "chipseq_", cell_type, "_", pwm_name, "_flank", flank, "_exp1.totalcount")
sites.df <- read.table(filename_sites, header = T, comment.char = "!", stringsAsFactors = F)
sites.df <- sites.df[, c("chr", "start", "end", "site", "pwmScore", "strand", "pValue", "mapability", "ChIP_mean")]
colnames(sites.df) = c("chr", "start", "end", "name", "pwm_score", "strand", "p_value", "mapability", "ChIP")
idx_select <- select_sites(sites.df, thresh_mapability, thresh_PWMscore)Select candidate sites
Select candidate sites with mapability >= 0.8
Select candidate sites with PWM score >= 10 sites.df <- sites.df[idx_select, ]
cat("Number of sites:", nrow(sites.df), "\n")Number of sites: 54533 counts_combined.m <- load_combine_counts(tf_name, pwm_name, dir_count_matrix)Loading count matrices ... counts_combined.m <- counts_combined.m[idx_select,]
## Clip extreme values
counts_combined.m[counts_combined.m > max_cuts] <- max_cuts
cat("Dimension of", dim(counts_combined.m), "\n")Dimension of 54533 440 if(nrow(counts_combined.m) != nrow(sites.df)){
stop("Sites not matched!")
}plot footprint profiles of highest occupancy sites
order_selected <- order(sites.df$ChIP, decreasing = T)[1:num_top_sites]
counts_selected.m <- counts_combined.m[order_selected,]
counts_profile <- apply(counts_selected.m, 2, mean)
par(mfrow = c(1,2))
counts <- counts_profile[1:(length(counts_profile)/2)]
plot(counts, type = "l", col = "blue", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "forward strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
counts <- counts_profile[(length(counts_profile)/2+1): length(counts_profile)]
plot(counts, type = "l", col = "red", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "reverse strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
Expand here to see past versions of unnamed-chunk-9-1.png:
| Version | Author | Date |
|---|---|---|
| 0e20593 | kevinlkx | 2018-08-29 |
## save counts matrix
rds_name <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/", tf_name, "/",
pwm_name, "_", cell_type, "_hg19_dnase_counts_selected_sites.rds")
saveRDS(counts_selected.m, rds_name)plot footprint profiles of most accessible sites
order_selected <- order(rowSums(counts_combined.m), decreasing = T)[1:num_top_sites]
counts_selected.m <- counts_combined.m[order_selected,]
counts_profile <- apply(counts_selected.m, 2, mean)
par(mfrow = c(1,2))
counts <- counts_profile[1:(length(counts_profile)/2)]
plot(counts, type = "l", col = "blue", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "forward strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
counts <- counts_profile[(length(counts_profile)/2+1): length(counts_profile)]
plot(counts, type = "l", col = "red", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "reverse strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
REST in K562 cell type
load DNase footprint data
cell_type <- "K562"
tf_name <- "REST"
pwm_name <- "REST_MA0138.2_1e-5"
dir_count_matrix <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/")
dir_sites_chip <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/ChIPSeq/")
filename_sites <- paste0(dir_sites_chip, "/", "chipseq_", cell_type, "_", pwm_name, "_flank", flank, "_exp1.totalcount")
sites.df <- read.table(filename_sites, header = T, comment.char = "!", stringsAsFactors = F)
sites.df <- sites.df[, c("chr", "start", "end", "site", "pwmScore", "strand", "pValue", "mapability", "ChIP_mean")]
colnames(sites.df) = c("chr", "start", "end", "name", "pwm_score", "strand", "p_value", "mapability", "ChIP")
idx_select <- select_sites(sites.df, thresh_mapability, thresh_PWMscore)Select candidate sites
Select candidate sites with mapability >= 0.8
Select candidate sites with PWM score >= 10 sites.df <- sites.df[idx_select, ]
cat("Number of sites:", nrow(sites.df), "\n")Number of sites: 54533 counts_combined.m <- load_combine_counts(tf_name, pwm_name, dir_count_matrix)Loading count matrices ... counts_combined.m <- counts_combined.m[idx_select,]
## Clip extreme values
counts_combined.m[counts_combined.m > max_cuts] <- max_cuts
cat("Dimension of", dim(counts_combined.m), "\n")Dimension of 54533 440 if(nrow(counts_combined.m) != nrow(sites.df)){
stop("Sites not matched!")
}plot footprint profiles of highest occupancy sites
order_selected <- order(sites.df$ChIP, decreasing = T)[1:num_top_sites]
counts_selected.m <- counts_combined.m[order_selected,]
counts_profile <- apply(counts_selected.m, 2, mean)
par(mfrow = c(1,2))
counts <- counts_profile[1:(length(counts_profile)/2)]
plot(counts, type = "l", col = "blue", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "forward strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
counts <- counts_profile[(length(counts_profile)/2+1): length(counts_profile)]
plot(counts, type = "l", col = "red", xlab = "Relative position (bp)", ylab = "Average counts",
main = "", xaxt = "n")
mtext(text = paste(tf_name, cell_type, "reverse strand"), side = 3, line = 1, cex = 1)
axis(1,at=c(1, flank+1, length(counts)-flank, length(counts)), labels=c(-flank, '','' ,flank),
cex.axis = 1, tck=-0.03, tick = T, cex = 1)
Expand here to see past versions of unnamed-chunk-12-1.png:
| Version | Author | Date |
|---|---|---|
| 0e20593 | kevinlkx | 2018-08-29 |
## save counts matrix
rds_name <- paste0(dir_data, "/DNase-seq_ENCODE/", cell_type, "/DNaseSeq/DNase_tagcount_matrix/", tf_name, "/",
pwm_name, "_", cell_type, "_hg19_dnase_counts_selected_sites.rds")
saveRDS(counts_selected.m, rds_name)Session information
sessionInfo()R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
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
loaded via a namespace (and not attached):
[1] workflowr_1.1.1 Rcpp_0.12.16 digest_0.6.15
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.21.0 magrittr_1.5 evaluate_0.10.1
[10] stringi_1.1.7 whisker_0.3-2 R.oo_1.22.0
[13] R.utils_2.6.0 rmarkdown_1.9 tools_3.4.3
[16] stringr_1.3.0 yaml_2.1.18 compiler_3.4.3
[19] htmltools_0.3.6 knitr_1.20 This reproducible R Markdown analysis was created with workflowr 1.1.1