-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathMethylKit.R
More file actions
88 lines (81 loc) · 6.08 KB
/
Copy pathMethylKit.R
File metadata and controls
88 lines (81 loc) · 6.08 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
#!/usr/bin/Rscript
###
library(BiocManager)
library(memoise)
library(sessioninfo)
library(devtools)
library(methylKit)
library(edmr)
file.list<-list("A1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"A2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"A3.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"A4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"A5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"A6.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"B1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"B2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"B4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"B5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"B6.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"C2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"C3.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"C4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"C6.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"D1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"D2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"D3.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"D4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"D5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"D6.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"E1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"E2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"E3.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"E4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"E5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F_B5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F3.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"F6.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"G1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"G2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"G4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"G5.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"G6.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"H1.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"H2.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"H3.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz",
"H4.pair1.truncated.gz_bismark_bt2_pe.multiple.deduplicated.bismark.cov.gz")
IDs<-list("A1","A2","A3","A4","A5","A6","B1","B2","B4","B5","B6","C2","C3","C4","C6","D1","D2","D3","D4","D5","D6","E1","E2","E3","E4","E5","F_B5","F1","F2","F3","F4","F5","F6","G1","G2","G4","G5","G6","H1","H2","H3","H4")
treatment<-c(0,1,0,0,1,0,1,1,0,1,1,1,0,0,1,1,0,0,1,1,0,0,0,1,1,1,0,1,0,1,0,0,1,1,1,1,0,0,1,1,0,1)
my_obj<-methRead(file.list, sample.id = IDs, assembly = "Chick", pipeline = "bismarkCoverage", treatment= treatment, context= "CpG", mincov=5)
filtered.my_obj_5X=filterByCoverage(my_obj,lo.count=5,lo.perc=NULL, hi.count=NULL,hi.perc=99.9)
meth.filtered_5X<-unite(filtered.my_obj_5X, destrand=F)
png(file="/home/projects/ku-cbd/data/HoloFood/Chicken_Epigenome/PCA_All_12288")
PCASamples(meth.filtered_5X)
dev.off()
IDs_Ross<-c("A1","A3","A4","A5","A6","B1","C3","C6","D1","D2","D3","D4","D5","D6","E3","E5","F_B5","F1","F2","F3","F5","F6","G4","G6","H1","H3")
treatment_Ross<-c(0,0,0,1,0,1,0,1,1,0,0,1,1,0,1,1,0,1,0,1,0,1,1,0,1,0)
my_obj_Ross<-reorganize(my_obj, IDs_Ross, treatment_Ross)
filtered.my_obj_Ross=filterByCoverage(my_obj_Ross,lo.count=5,lo.perc=NULL, hi.count=NULL,hi.perc=99.9)
meth.filtered_Ross<-unite(filtered.my_obj_Ross, destrand=F)
png(file="/home/projects/ku-cbd/data/HoloFood/Chicken_Epigenome/PCA_Ross_17231")
PCASamples(meth.filtered_Ross)
dev.off()
IDs_Cobb<-c("A2","B2","B4","B5","B6","C2","C4","E1","E2","E4","F4","G1","G2","G5","H2","H4")
treatment_Cobb<-c(1,1,0,1,1,1,0,0,0,1,0,1,1,0,1,1)
my_obj_Cobb<-reorganize(my_obj, IDs_Cobb, treatment_Cobb)
filtered.my_obj_Cobb=filterByCoverage(my_obj_Cobb,lo.count=5,lo.perc=NULL, hi.count=NULL,hi.perc=99.9)
meth.filtered_Cobb<-unite(filtered.my_obj_Cobb, destrand=F)
png(file="/home/projects/ku-cbd/data/HoloFood/Chicken_Epigenome/PCA_Cobb_22398")
PCASamples(meth.filtered_Cobb)
dev.off()
rm(my_obj)
rm(my_obj_Ross)
rm(my_obj_Cobb)
rm(filtered.my_obj_5X)
rm(filtered.my_obj_Ross)
rm(filtered.my_obj_Cobb)
save.image("/home/projects/ku-cbd/data/HoloFood/Chicken_Epigenome/Chicken.RData")