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ENCODE_chip_process.R
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ENCODE_chip_process.R
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# GM binary repeat of juan et al., data
library(dplyr)
library(GenomicRanges)
library(tidyverse)
library(stringr)
metadata <- read.delim(file = "~/Data/GM12878/ENCODE/GM12878_ENCODE/metadata.tsv", header = T, sep = "\t")
metadata %>%
filter(Output.type == "peaks" & File.assembly == "hg19") %>%
select(File.accession, Experiment.target, Biological.replicate.s.)
ChIP_without_replicate <- metadata %>%
filter(Output.type == "peaks" & File.assembly == "hg19") %>%
filter(Biological.replicate.s. =="") %>%
dplyr::select(File.accession, Experiment.target)
Replicated <- metadata %>%
filter(Output.type == "peaks" & File.assembly == "hg19") %>%
filter(Biological.replicate.s. =="1, 2") %>%
dplyr::select(File.accession, Experiment.target)
ENCODE <- rbind(ChIP_without_replicate, Replicated)
# used something like this, not exactly because had to convert back to bed.gz but used a loop to convert all files that had a match in ENCODE.txt to the ChIP-seq name (e.g MYC instead of long ENCODE identifier)
# for(i in 1:nrow(ENCODE)){
# # Get the file name
# file_name <- ENCODE[i,1]
# # Construct the full file path
# file_path <- file.path("~/Data/GM12878/ENCODE/GM12878_ENCODE/CopyOfIn_use/", paste(file_name,"bed", sep = "."))
# # Check if the file exists
# if(file.exists(file_path)){
# # Construct the new file path
# new_file_path <- file.path("/home/dankent/Data/GM12878/ENCODE/In_use/", paste(ENCODE[i,2],"bed.gz", sep = "."))
# }
# }
# Then this in command line
# while IFS=$'\t' read -r oldname newname; do
# mv "$oldname" "$newname"
# done < ~/Data/MouseESC/Juan et al., data/GM12878_ENCODE/ENCODE.txt
# make this for creating binary files with ChromHMM
ENCODE.txt <- read.delim(file = "~/Data/GM12878/ENCODE/In_use/ENCODE.txt", header = F, sep = "\t")
ENCODE.txt$V2 <- paste0(ENCODE.txt$V2, ".bed")
ENCODE.txt <- ENCODE.txt %>% mutate(GM = "GM12878", .before = V1) %>%
select(GM, V2)
ENCODE.txt <- ENCODE.txt %>% mutate(name = sub("-.*", "", ENCODE.txt$V2), .before = V2)
ENCODE.txt <- readr::write_tsv(ENCODE.txt, file = "/home/dankent/Data/GM12878/ENCODE/In_use/myDataFile_ENCODE.txt", col_names = F)
# run in command line with
# java -jar ChromHMM.jar BinarizeBed -peaks CHROMSIZES/hg19.txt ~/Data/GM12878/ENCODE/In_use ~/Data/GM12878/ENCODE/In_use/myDataFile_ENCODE.txt ~/Data/GM12878/ENCODE/In_use/binary/
# look
BHLHE40 <- read.delim(file = "~/Data/GM12878/ENCODE/In_use/BHLHE40-human.bed", header = F, sep = "\t")
# read in to R and add appropriate columns
Chr1_binary <- read.delim(file = "~/Data/GM12878/ENCODE/In_use/binary/GM12878_chr1_binary.txt", header = F, sep = "\t")
Chr1_binary <- Chr1_binary[-1,]
colnames(Chr1_binary) <- Chr1_binary[1,]
Chr1_binary <- Chr1_binary[-1,]
# nrow(Chr1_binary)
# [1] 1246253
# read in genome size to create ranges
hg19_size <- read.delim("~/progs/ChromHMM-1.18/CHROMSIZES/hg19.txt", header = F)
hg19_size <- hg19_size[1:24,]
chr1 <- data.frame(start = seq(0, hg19_size[1,2], by = 200))
chr1 <- data.frame(seqnames = "chr1", start = (head(chr1,-1)), end = chr1[-1,])
chr1 <- makeGRangesFromDataFrame(chr1)
# length(chr1)
# [1] 1246253
# SAME AS ABOVE SO EACH BIN MUST MATCH UP PERFECTLY! WOOOOOO
# now convert the above into a loop-able function
#split into chr for lapply function to create ranges
hg19_size_list <- split(hg19_size, f = hg19_size$V1)
# function to make ranges
Create_chr_ranges <- function(list){
x <- list[] # extract each member
y <- data.frame(start = seq(0, x[,2], by = 200)) # seq along the entire length of the chrom and split into 200bp bins
y <- data.frame(seqnames = x[,1], start = head(y, -1), end = y[-1,]) # make a data frame of the chr, start (- last start as this is the last row end), end (take away first end as this is 0 and the first start)
}
Chr_ranges <- lapply(hg19_size_list, Create_chr_ranges)
# read in all files from chromHMM
Chr10_binary <- read.delim(file = "~/Data/GM12878/ENCODE/In_use/binary/GM12878_chr10_binary.txt", header = F, sep = "\t")
Chr1_binary <- Chr1_binary[-1,]
colnames(Chr1_binary) <- Chr1_binary[1,]
Chr1_binary <- Chr1_binary[-1,]
# list files in directory
list_files <- list.files("~/Data/GM12878/ENCODE/In_use/binary", pattern="*.txt", full.names=TRUE)
#read 'em all! and remove the weird names that ChromHMM adds to the first row
for (i in seq_along(1:length(list_files))) {
# read the data
data_import <- read.delim( paste0( "", list_files[i]), na = c( "NA", ""), header = F) # create object name based on filename
data_import <- data_import[-1,]
colnames(data_import) <- data_import[1,]
data_import <- data_import[-1,]
dataframe_name <- tolower( paste0("binary_", str_match( # function to find a matching string
list_files[i], "8_(.*?)_b" # extract string between "8_" and "_b" in filename
)[, 2] # extract second element of the str_match() output
)
)
# give the temporary data_import object the dataframe_name
assign(dataframe_name, data_import)
# output the filename and object name in the console
print(list_files[i])
print(dataframe_name)
}
head(binary_chr1) # wahooooo! It works
## now add the chr, start and end from hg19_sizes to the binary files
Chr1_combined <- cbind(Chr_ranges$chr1, binary_chr1)
Chr2_combined <- cbind(Chr_ranges$chr2, binary_chr2)
Chr3_combined <- cbind(Chr_ranges$chr3, binary_chr3)
Chr4_combined <- cbind(Chr_ranges$chr4, binary_chr4)
Chr5_combined <- cbind(Chr_ranges$chr5, binary_chr5)
Chr6_combined <- cbind(Chr_ranges$chr6, binary_chr6)
Chr7_combined <- cbind(Chr_ranges$chr7, binary_chr7)
Chr8_combined <- cbind(Chr_ranges$chr8, binary_chr8)
Chr9_combined <- cbind(Chr_ranges$chr9, binary_chr9)
Chr10_combined <- cbind(Chr_ranges$chr10, binary_chr10)
Chr11_combined <- cbind(Chr_ranges$chr11, binary_chr11)
Chr12_combined <- cbind(Chr_ranges$chr12, binary_chr12)
Chr13_combined <- cbind(Chr_ranges$chr13, binary_chr13)
Chr14_combined <- cbind(Chr_ranges$chr14, binary_chr14)
Chr15_combined <- cbind(Chr_ranges$chr15, binary_chr15)
Chr16_combined <- cbind(Chr_ranges$chr16, binary_chr16)
Chr17_combined <- cbind(Chr_ranges$chr17, binary_chr17)
Chr18_combined <- cbind(Chr_ranges$chr18, binary_chr18)
Chr19_combined <- cbind(Chr_ranges$chr19, binary_chr19)
Chr20_combined <- cbind(Chr_ranges$chr20, binary_chr20)
Chr21_combined <- cbind(Chr_ranges$chr21, binary_chr21)
Chr22_combined <- cbind(Chr_ranges$chr22, binary_chr22)
GM12878_ENCODE_features <- rbind(Chr1_combined,
Chr2_combined,
Chr3_combined,
Chr4_combined,
Chr5_combined,
Chr6_combined,
Chr7_combined,
Chr8_combined,
Chr9_combined,
Chr10_combined,
Chr11_combined,
Chr12_combined,
Chr13_combined,
Chr14_combined,
Chr15_combined,
Chr16_combined,
Chr17_combined,
Chr18_combined,
Chr19_combined,
Chr20_combined,
Chr21_combined,
Chr22_combined)
rm(list=ls(pattern="*_combined"))
rm(list=ls(pattern="binary*"))
readr::write_tsv(x = GM12878_ENCODE_features, file = "~/Data/GM12878/ENCODE/GM12878_ENCODE_features.tsv", col_names = T)