cran_mirror <- Sys.getenv("R_CRAN_MIRROR", "http://cran.rstudio.com/") options(repos = cran_mirror) if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("methylKit") library(BiocManager) library(stringi) library(pacman) library(methylKit) library(ade4) library(FactoMineR) library(devtools) library(factoextra) library(tibble) library(caret) file.list <- list("/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-105_AHCY7CDSXC_S101_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-111_AHCY7CDSXC_S20_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-112_AHCY7CDSXC_S58_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-113_AHCY7CDSXC_S47_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-118_AHCY7CDSXC_S91_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-142_AHCY7CDSXC_S32_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-143_AHCY7CDSXC_S102_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-146_AHCY7CDSXC_S97_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-147_AHCY7CDSXC_S95_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-176_AHCY7CDSXC_S92_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-178_AHCY7CDSXC_S21_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-180_AHCY7CDSXC_S98_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-182_AHCY7CDSXC_S36_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-183_AHCY7CDSXC_S31_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-184_AHCY7CDSXC_S69_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-27_AHCY7CDSXC_S82_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-28_AHCY7CDSXC_S89_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-68_AHCY7CDSXC_S110_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/21-71_AHCY7CDSXC_S93_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-01_AHCY7CDSXC_S49_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-03_AHCY7CDSXC_S104_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-05_AHCY7CDSXC_S100_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-10_AHCY7CDSXC_S71_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-11_AHCY7CDSXC_S60_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-12_AHCY7CDSXC_S63_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-13_AHCY7CDSXC_S50_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-14_AHCY7CDSXC_S61_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-18_AHCY7CDSXC_S80_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-19_AHCY7CDSXC_S96_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-20_AHCY7CDSXC_S39_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-28_AHCY7CDSXC_S35_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-37_AHCY7CDSXC_S72_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-38_AHCY7CDSXC_S90_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-39_AHCY7CDSXC_S34_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-43_AHCY7CDSXC_S52_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-44_AHCY7CDSXC_S73_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-45_AHCY7CDSXC_S19_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-49_AHCY7CDSXC_S87_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-50_AHCY7CDSXC_S48_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-51_AHCY7CDSXC_S26_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/22-52_AHCY7CDSXC_S55_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-27_AHCY7CDSXC_S79_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-28_AHCY7CDSXC_S74_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-29_AHCY7CDSXC_S33_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-30_AHCY7CDSXC_S27_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-32_AHCY7CDSXC_S78_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-33_AHCY7CDSXC_S77_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-35_AHCY7CDSXC_S53_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-36_AHCY7CDSXC_S83_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-37_AHCY7CDSXC_S76_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-38_AHCY7CDSXC_S37_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-39_AHCY7CDSXC_S38_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-40_AHCY7CDSXC_S59_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-41_AHCY7CDSXC_S30_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-42_AHCY7CDSXC_S56_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-43_AHCY7CDSXC_S54_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-44_AHCY7CDSXC_S43_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-45_AHCY7CDSXC_S86_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-46_AHCY7CDSXC_S45_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-47_AHCY7CDSXC_S99_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-48_AHCY7CDSXC_S17_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-49_AHCY7CDSXC_S81_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-50_AHCY7CDSXC_S85_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-52_AHCY7CDSXC_S103_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-53_AHCY7CDSXC_S68_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-54_AHCY7CDSXC_S105_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam","/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-55_AHCY7CDSXC_S22_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-56_AHCY7CDSXC_S46_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-57_AHCY7CDSXC_S75_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-58_AHCY7CDSXC_S40_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-59_AHCY7CDSXC_S51_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-60_AHCY7CDSXC_S44_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-61_AHCY7CDSXC_S57_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-62_AHCY7CDSXC_S66_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-63_AHCY7CDSXC_S94_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam", "/home/jbelik/RRBS/Clock/Data/Bismark_results/New/23-64_AHCY7CDSXC_S62_L001_R1_001_val_1_bismark_bt2_pe.sorted.bam") #it takes a lot of time myobj <- processBismarkAln(file.list, sample.id=list("21-105", "21-111", "21-112", "21-113", "21-118", "21-142", "21-143", "21-146", "21-147","21-176", "21-178", "21-180", "21-182", "21-183", "21-184", "21-27", "21-28", "21-68", "21-71", "22-01", "22-03", "22-05", "22-10","22-11", "22-12", "22-13", "22-14", "22-18", "22-19", "22-20", "22-28", "22-37", "22-38","22-39", "22-43", "22-44", "22-45", "22-49", "22-50", "22-51", "22-52", "23-27", "23-28","23-29", "23-30", "23-32", "23-33", "23-35", "23-36", "23-37", "23-38", "23-39", "23-40","23-41", "23-42", "23-43", "23-44", "23-45", "23-46", "23-47", "23-48", "23-49", "23-50","23-52", "23-53", "23-54", "23-55", "23-56", "23-57", "23-58", "23-59", "23-60", "23-61","23-62", "23-63", "23-64"), assembly="ASM164957v2", treatment=c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1), read.context="CpG", save.folder = getwd(), mincov = 10 ) saveRDS(myobj, file="/home/jbelik/RRBS/Clock/Data/Bismark_results/Clock-new-young.RDS")