In ZW-xjtlu/exomePeak2Test: Easy test of the exomePeak2 performance.

knitr::opts_chunk$set(echo = TRUE)

submit exomepeak2 peakcalling on server

Test peak calling functions

library(exomePeak2Test)

ColData_hg19 <- read.csv("~/merip_bam/coldata_hg19.csv")

parallel_peak_calling(
coldata = ColData_hg19[ColData_hg19$Perturbation == "C",],
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_gmmGC",
parallel_num = 9,
single_base = F
)


library(exomePeak2Test)

ColData_hg19 <- read.csv("~/merip_bam/coldata_hg19.csv")

parallel_peak_calling(
coldata = ColData_hg19[ColData_hg19$Perturbation == "C",],
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_annot",
parallel_num = 9,
front_name = "annot_",
single_base = T
)

library(exomePeak2Test)

ColData_hg19 <- read.csv("~/merip_bam/coldata_hg19.csv")

parallel_peak_calling(
coldata = ColData_hg19[ColData_hg19$Perturbation == "C",],
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_annot",
parallel_num = 9,
front_name = "pc_unifGC_",
single_base = F
)


library(exomePeak2Test)

ColData_hg19 <- read.csv("~/merip_bam/coldata_hg19.csv")

parallel_peak_calling(
coldata = ColData_hg19[ColData_hg19$Perturbation == "C",],
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/pc_noGC",
parallel_num = 9,
front_name = "pc_noGC_",
single_base = F,
GC_correct = F
)

library(exomePeak2Test)
dir.create("~/exomepeak2_test/test_pc_m6Aprior_noGC")
dir.create("~/exomepeak2_test/test_pc_m6Aprior_uniformGC")
dir.create("~/exomepeak2_test/test_pc_m6Aprior_bgGC")

ColData_test <- read.csv("~/exomepeak2_test/coldata_hg19_test.csv")

setwd("~/exomepeak2_test/test_pc_m6Aprior_noGC")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_m6Aprior_noGC",
parallel_num = 3,
single_base = F,
background = "m6Aseq_prior",
GC_correct = F,
correct_GC_bg = F
) #Submmited 10:13 AM

setwd("~/exomepeak2_test/test_pc_m6Aprior_uniformGC")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_m6Aprior_uniformGC",
parallel_num = 2,
single_base = F,
background = "m6Aseq_prior",
GC_correct = T,
correct_GC_bg = F
)

setwd("~/exomepeak2_test/test_pc_m6Aprior_bgGC")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_m6Aprior_bgGC",
parallel_num = 2,
single_base = F,
background = "m6Aseq_prior",
GC_correct = T,
correct_GC_bg = T
)

Test RDEMPTION

library(exomePeak2Test)

ColData_test <- read.csv("~/exomepeak2_test/coldata_hg19_test.csv")

dir.create("~/exomepeak2_test/test_pc_GMMgc")

setwd("~/exomepeak2_test/test_pc_GMMgc")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_redemption2",
parallel_num = 2,
single_base = F,
background = "Gaussian_mixture",
GC_correct = T,
correct_GC_bg = T
)


library(exomePeak2Test)

ColData_test <- read.csv("~/exomepeak2_test/coldata_hg19_test.csv")

dir.create("~/exomepeak2_test/test_pc_GMMgc")

setwd("~/exomepeak2_test/test_pc_GMMgc")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_GMMgc",
parallel_num = 2,
single_base = F,
background = "m6Aseq_prior",
GC_correct = T,
correct_GC_bg = T
)

dir.create("~/exomepeak2_test/test_pc_m6APgc")

setwd("~/exomepeak2_test/test_pc_m6APgc")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_m6APgc",
parallel_num = 2,
single_base = F,
background = "m6Aseq_prior",
GC_correct = T,
correct_GC_bg = T
)

dir.create("~/exomepeak2_test/test_pc_UNIFgc")

setwd("~/exomepeak2_test/test_pc_UNIFgc")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_UNIFgc",
parallel_num = 2,
single_base = F,
background = "all",
GC_correct = T,
correct_GC_bg = T
)

library(exomePeak2Test)

ColData_test <- read.csv("~/exomepeak2_test/coldata_hg19_test.csv")

dir.create("~/exomepeak2_test/test_pc_GMMgc_noqtnorm")

setwd("~/exomepeak2_test/test_pc_GMMgc_noqtnorm")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_GMMgc_noqtnorm",
parallel_num = 2,
single_base = F,
background = "m6Aseq_prior",
GC_correct = T,
correct_GC_bg = T,
qtnorm = F
)

dir.create("~/exomepeak2_test/test_pc_m6APgc_noqtnorm")

setwd("~/exomepeak2_test/test_pc_m6APgc_noqtnorm")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_m6APgc_noqtnorm",
parallel_num = 2,
single_base = F,
background = "m6Aseq_prior",
GC_correct = T,
correct_GC_bg = T,
qtnorm = F
)

dir.create("~/exomepeak2_test/test_pc_UNIFgc_noqtnorm")

setwd("~/exomepeak2_test/test_pc_UNIFgc_noqtnorm")

parallel_peak_calling(
coldata = ColData_test,
bam_dir = "~/merip_bam",
save_dir = "~/exomepeak2_test/test_pc_UNIFgc_noqtnorm",
parallel_num = 2,
single_base = F,
background = "all",
GC_correct = T,
correct_GC_bg = T,
qtnorm = F
)