-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathScript Clump Plink.R
More file actions
292 lines (269 loc) · 15.8 KB
/
Script Clump Plink.R
File metadata and controls
292 lines (269 loc) · 15.8 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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
# load libraries and functions
source("./Script dependencies.R")
# GWAS EA
ea_gwas_full <- fread("./data/GWAS_EA_excl23andMe.txt",
stringsAsFactors = FALSE,
data.table = FALSE,
fill = TRUE)
colnames(ea_gwas_full)[1] <- "SNP"
colnames(ea_gwas_full)[9] <- "P"
fwrite(ea_gwas_full,
file = "./data/clump/GWAS_EA_excl23andMe_colname_fix.txt",
sep = " ")
# 1000 Genomes data
system("tar -xvzf ./data/clump/1000G_Phase3_plinkfiles.tgz --directory ./data/clump/")
# if plink acting up, try
system("bash ./cd_internship.sh") # may not work, or cd in linux commandline
# running ./plink2 gives trouble, however shellscript works fine
# run shell script plink_all.sh for clumping results, call plink.sh for chr 1-22
# old data
system("bash ./plink_clump_all.sh")
# new data
system("bash ./plink_clump_all_newdata.sh")
# plink clumping results old data
clump_chr1.old <- fread("./data/clump/results/EA_clumped.chr.1.clumped")
clump_chr2.old <- fread("./data/clump/results/EA_clumped.chr.2.clumped")
clump_chr3.old <- fread("./data/clump/results/EA_clumped.chr.3.clumped")
clump_chr4.old <- fread("./data/clump/results/EA_clumped.chr.4.clumped")
clump_chr5.old <- fread("./data/clump/results/EA_clumped.chr.5.clumped")
clump_chr6.old <- fread("./data/clump/results/EA_clumped.chr.6.clumped")
clump_chr7.old <- fread("./data/clump/results/EA_clumped.chr.7.clumped")
clump_chr8.old <- fread("./data/clump/results/EA_clumped.chr.8.clumped")
clump_chr9.old <- fread("./data/clump/results/EA_clumped.chr.9.clumped")
clump_chr10.old <- fread("./data/clump/results/EA_clumped.chr.10.clumped")
clump_chr11.old <- fread("./data/clump/results/EA_clumped.chr.11.clumped")
clump_chr12.old <- fread("./data/clump/results/EA_clumped.chr.12.clumped")
clump_chr13.old <- fread("./data/clump/results/EA_clumped.chr.13.clumped")
clump_chr14.old <- fread("./data/clump/results/EA_clumped.chr.14.clumped")
clump_chr15.old <- fread("./data/clump/results/EA_clumped.chr.15.clumped")
clump_chr16.old <- fread("./data/clump/results/EA_clumped.chr.16.clumped")
clump_chr17.old <- fread("./data/clump/results/EA_clumped.chr.17.clumped")
clump_chr18.old <- fread("./data/clump/results/EA_clumped.chr.18.clumped")
clump_chr19.old <- fread("./data/clump/results/EA_clumped.chr.19.clumped")
clump_chr20.old <- fread("./data/clump/results/EA_clumped.chr.20.clumped")
clump_chr21.old <- fread("./data/clump/results/EA_clumped.chr.21.clumped")
clump_chr22.old <- fread("./data/clump/results/EA_clumped.chr.22.clumped")
# plink clumping results
clump_chr1 <- fread("./data/clump/results_newdata/EA_clumped.chr.1.clumped")
clump_chr2 <- fread("./data/clump/results_newdata/EA_clumped.chr.2.clumped")
clump_chr3 <- fread("./data/clump/results_newdata/EA_clumped.chr.3.clumped")
clump_chr4 <- fread("./data/clump/results_newdata/EA_clumped.chr.4.clumped")
clump_chr5 <- fread("./data/clump/results_newdata/EA_clumped.chr.5.clumped")
clump_chr6 <- fread("./data/clump/results_newdata/EA_clumped.chr.6.clumped")
clump_chr7 <- fread("./data/clump/results_newdata/EA_clumped.chr.7.clumped")
clump_chr8 <- fread("./data/clump/results_newdata/EA_clumped.chr.8.clumped")
clump_chr9 <- fread("./data/clump/results_newdata/EA_clumped.chr.9.clumped")
clump_chr10 <- fread("./data/clump/results_newdata/EA_clumped.chr.10.clumped")
clump_chr11 <- fread("./data/clump/results_newdata/EA_clumped.chr.11.clumped")
clump_chr12 <- fread("./data/clump/results_newdata/EA_clumped.chr.12.clumped")
clump_chr13 <- fread("./data/clump/results_newdata/EA_clumped.chr.13.clumped")
clump_chr14 <- fread("./data/clump/results_newdata/EA_clumped.chr.14.clumped")
clump_chr15 <- fread("./data/clump/results_newdata/EA_clumped.chr.15.clumped")
clump_chr16 <- fread("./data/clump/results_newdata/EA_clumped.chr.16.clumped")
clump_chr17 <- fread("./data/clump/results_newdata/EA_clumped.chr.17.clumped")
clump_chr18 <- fread("./data/clump/results_newdata/EA_clumped.chr.18.clumped")
clump_chr19 <- fread("./data/clump/results_newdata/EA_clumped.chr.19.clumped")
clump_chr20 <- fread("./data/clump/results_newdata/EA_clumped.chr.20.clumped")
clump_chr21 <- fread("./data/clump/results_newdata/EA_clumped.chr.21.clumped")
clump_chr22 <- fread("./data/clump/results_newdata/EA_clumped.chr.22.clumped")
# bind all chromosomes
clump_res <- rbind.data.frame(clump_chr1, clump_chr2, clump_chr3, clump_chr4,
clump_chr5, clump_chr6, clump_chr7, clump_chr8,
clump_chr9, clump_chr10, clump_chr11, clump_chr12,
clump_chr13, clump_chr14, clump_chr15, clump_chr16,
clump_chr17, clump_chr18, clump_chr19, clump_chr20,
clump_chr21, clump_chr22)
rm(clump_chr1, clump_chr2, clump_chr3, clump_chr4,
clump_chr5, clump_chr6, clump_chr7, clump_chr8,
clump_chr9, clump_chr10, clump_chr11, clump_chr12,
clump_chr13, clump_chr14, clump_chr15, clump_chr16,
clump_chr17, clump_chr18, clump_chr19, clump_chr20,
clump_chr21, clump_chr22)
clump_res <- clump_res %>%
separate(., SP2, into = as.character(c(1:941)), sep = ",") %>%
as.matrix()
clump_res[, 12:ncol(clump_res)] <- substr(as.matrix(clump_res[, 12:ncol(clump_res)]), 1, nchar(as.matrix(clump_res[, 12:ncol(clump_res)])) - 3)
clump_res <- clump_res %>%
as.data.frame() %>%
unite(., SP2, 12:ncol(clump_res), sep = ", ", na.rm = TRUE)
#fwrite(clump_res, file = "./data/LD/EA_clumped_full.txt")
# ciseQTL
ciseQTLs <- fread("./data/eQTL/2019-12-11-cis-eQTLsFDR0.05-ProbeLevel-CohortInfoRemoved-BonferroniAdded.txt.gz",
stringsAsFactors = FALSE,
data.table = FALSE,
fill = TRUE)
# transeQTL
transeQTLs <- fread("./data/eQTL/2018-09-04-trans-eQTLsFDR0.05-CohortInfoRemoved-BonferroniAdded.txt.gz",
stringsAsFactors = FALSE,
data.table = FALSE,
fill = TRUE)
# selecting lead SNPs per gene (& per chromosome for trans) for cis- & transeQTLs
start <- Sys.time()
eQTLs_cis <- eQTL_finder(ciseQTLs, eQTL = "cis")
Sys.time() - start # time: 1.085 hours for full dataset
eQTLs_cis$Gene %>% unique() %>% length(); ciseQTLs$Gene %>% unique() %>% length() # all 16987 genes present
eQTLs_cis$SNP %>% unique() %>% length(); ciseQTLs$SNP %>% unique() %>% length() # 16290 of 3663456 SNPs are lead SNPs
eQTLs_cis_duplicated <- eQTLs_cis[duplicated(eQTLs_cis$SNP),]
eQTLs_cis_duplicates <- eQTLs_cis %>%
filter(., SNP %in% eQTLs_cis_duplicated$SNP); eQTLs_cis_duplicated$SNP %>% unique() %>% length(); rm(eQTLs_cis_duplicated)
start <- Sys.time()
eQTLs_trans <- eQTL_finder(transeQTLs, eQTL = "trans")
Sys.time() - start # time: 1.56 minutes for full dataset
eQTLs_trans$Gene %>% unique() %>% length(); transeQTLs$Gene %>% unique() %>% length() # all 6298 genes present
eQTLs_trans$SNP %>% unique() %>% length(); transeQTLs$SNP %>% unique() %>% length() # 2639 of 3853 SNPs are lead SNPs
eQTLs_trans$SNPChr %>% unique() %>% length(); transeQTLs$SNPChr %>% unique() %>% length()
eQTLs_trans_duplicated <- eQTLs_trans[duplicated(eQTLs_trans$SNP),]
eQTLs_trans_duplicates <- eQTLs_trans %>%
filter(., SNP %in% eQTLs_trans_duplicated$SNP); eQTLs_trans_duplicated$SNP %>% unique() %>% length(); rm(eQTLs_trans_duplicated)
# write to .txt
#fwrite(eQTLs_cis, file = "./data/LD/Lead_ciseQTL.txt")
#fwrite(eQTLs_trans, file = "./data/LD/Lead_transeQTL.txt")
eQTLs_cis <- fread("./data/LD/Lead_ciseQTL.txt")
eQTLs_trans <- fread("./data/LD/Lead_transeQTL.txt")
clump_res <- fread("./data/LD/EA_clumped_full.txt")
eQTLs_cis$SNP %>%
unique() %>%
as.data.frame() %>%
as.list() %>%
fwrite(., file = "./data/LD/SNPlist_lead_ciseQTL.txt", col.names = FALSE)
eQTLs_trans$SNP %>%
unique() %>%
as.data.frame() %>%
as.list() %>%
fwrite(., file = "./data/LD/SNPlist_lead_transeQTL.txt", col.names = FALSE)
clump_res$SNP %>%
as.data.frame() %>%
as.list() %>%
fwrite(., file = "./data/LD/SNPlist_EA_clumped.txt", col.names = FALSE)
# plink calculate LD
# old data
system("bash ./plink_ld_calc_all.sh cis SNPlist_lead_ciseQTL.txt")
system("bash ./plink_ld_calc_all.sh trans SNPlist_lead_transeQTL.txt")
# new data
system("bash ./plink_ld_calc_all_newdata.sh cis SNPlist_lead_ciseQTL.txt")
system("bash ./plink_ld_calc_all_newdata.sh trans SNPlist_lead_transeQTL.txt")
# LD files
# plink clumping results
# LD ciseQTLs old data
LD_cis_chr1.old <- fread("./data/LD/results/LD.cis.1.ld")
LD_cis_chr2.old <- fread("./data/LD/results/LD.cis.2.ld")
LD_cis_chr3.old <- fread("./data/LD/results/LD.cis.3.ld")
LD_cis_chr4.old <- fread("./data/LD/results/LD.cis.4.ld")
LD_cis_chr5.old <- fread("./data/LD/results/LD.cis.5.ld")
LD_cis_chr6.old <- fread("./data/LD/results/LD.cis.6.ld")
LD_cis_chr7.old <- fread("./data/LD/results/LD.cis.7.ld")
LD_cis_chr8.old <- fread("./data/LD/results/LD.cis.8.ld")
LD_cis_chr9.old <- fread("./data/LD/results/LD.cis.9.ld")
LD_cis_chr10.old <- fread("./data/LD/results/LD.cis.10.ld")
LD_cis_chr11.old <- fread("./data/LD/results/LD.cis.11.ld")
LD_cis_chr12.old <- fread("./data/LD/results/LD.cis.12.ld")
LD_cis_chr13.old <- fread("./data/LD/results/LD.cis.13.ld")
LD_cis_chr14.old <- fread("./data/LD/results/LD.cis.14.ld")
LD_cis_chr15.old <- fread("./data/LD/results/LD.cis.15.ld")
LD_cis_chr16.old <- fread("./data/LD/results/LD.cis.16.ld")
LD_cis_chr17.old <- fread("./data/LD/results/LD.cis.17.ld")
LD_cis_chr18.old <- fread("./data/LD/results/LD.cis.18.ld")
LD_cis_chr19.old <- fread("./data/LD/results/LD.cis.19.ld")
LD_cis_chr20.old <- fread("./data/LD/results/LD.cis.20.ld")
LD_cis_chr21.old <- fread("./data/LD/results/LD.cis.21.ld")
LD_cis_chr22.old <- fread("./data/LD/results/LD.cis.22.ld")
LD_cis_res.old <- rbind.data.frame(LD_cis_chr1.old, LD_cis_chr2.old, LD_cis_chr3.old, LD_cis_chr4.old,
LD_cis_chr5.old, LD_cis_chr6.old, LD_cis_chr7.old, LD_cis_chr8.old,
LD_cis_chr9.old, LD_cis_chr10.old, LD_cis_chr11.old, LD_cis_chr12.old,
LD_cis_chr13.old, LD_cis_chr14.old, LD_cis_chr15.old, LD_cis_chr16.old,
LD_cis_chr17.old, LD_cis_chr18.old, LD_cis_chr19.old, LD_cis_chr20.old,
LD_cis_chr21.old, LD_cis_chr22.old)
# LD ciseQTLs new data
LD_cis_chr1 <- fread("./data/LD/results_newdata/LD.cis.1.ld")
LD_cis_chr2 <- fread("./data/LD/results_newdata/LD.cis.2.ld")
LD_cis_chr3 <- fread("./data/LD/results_newdata/LD.cis.3.ld")
LD_cis_chr4 <- fread("./data/LD/results_newdata/LD.cis.4.ld")
LD_cis_chr5 <- fread("./data/LD/results_newdata/LD.cis.5.ld")
LD_cis_chr6 <- fread("./data/LD/results_newdata/LD.cis.6.ld")
LD_cis_chr7 <- fread("./data/LD/results_newdata/LD.cis.7.ld")
LD_cis_chr8 <- fread("./data/LD/results_newdata/LD.cis.8.ld")
LD_cis_chr9 <- fread("./data/LD/results_newdata/LD.cis.9.ld")
LD_cis_chr10 <- fread("./data/LD/results_newdata/LD.cis.10.ld")
LD_cis_chr11 <- fread("./data/LD/results_newdata/LD.cis.11.ld")
LD_cis_chr12 <- fread("./data/LD/results_newdata/LD.cis.12.ld")
LD_cis_chr13 <- fread("./data/LD/results_newdata/LD.cis.13.ld")
LD_cis_chr14 <- fread("./data/LD/results_newdata/LD.cis.14.ld")
LD_cis_chr15 <- fread("./data/LD/results_newdata/LD.cis.15.ld")
LD_cis_chr16 <- fread("./data/LD/results_newdata/LD.cis.16.ld")
LD_cis_chr17 <- fread("./data/LD/results_newdata/LD.cis.17.ld")
LD_cis_chr18 <- fread("./data/LD/results_newdata/LD.cis.18.ld")
LD_cis_chr19 <- fread("./data/LD/results_newdata/LD.cis.19.ld")
LD_cis_chr20 <- fread("./data/LD/results_newdata/LD.cis.20.ld")
LD_cis_chr21 <- fread("./data/LD/results_newdata/LD.cis.21.ld")
LD_cis_chr22 <- fread("./data/LD/results_newdata/LD.cis.22.ld")
LD_cis_res <- rbind.data.frame(LD_cis_chr1, LD_cis_chr2, LD_cis_chr11, LD_cis_chr16)# %>%
# filter(., SNP_A != SNP_B)
rm(LD_cis_chr1, LD_cis_chr2, LD_cis_chr3, LD_cis_chr4,
LD_cis_chr5, LD_cis_chr6, LD_cis_chr7, LD_cis_chr8,
LD_cis_chr9, LD_cis_chr10, LD_cis_chr11, LD_cis_chr12,
LD_cis_chr13, LD_cis_chr14, LD_cis_chr15, LD_cis_chr16,
LD_cis_chr17, LD_cis_chr18, LD_cis_chr19, LD_cis_chr20,
LD_cis_chr21, LD_cis_chr22)
# LD transeQTLs
LD_trans_chr1 <- fread("./data/LD/results_newdata/LD.trans.1.ld")
LD_trans_chr2 <- fread("./data/LD/results_newdata/LD.trans.2.ld")
LD_trans_chr3 <- fread("./data/LD/results_newdata/LD.trans.3.ld")
LD_trans_chr4 <- fread("./data/LD/results_newdata/LD.trans.4.ld")
LD_trans_chr5 <- fread("./data/LD/results_newdata/LD.trans.5.ld")
LD_trans_chr6 <- fread("./data/LD/results_newdata/LD.trans.6.ld")
LD_trans_chr7 <- fread("./data/LD/results_newdata/LD.trans.7.ld")
LD_trans_chr8 <- fread("./data/LD/results_newdata/LD.trans.8.ld")
LD_trans_chr9 <- fread("./data/LD/results_newdata/LD.trans.9.ld")
LD_trans_chr10 <- fread("./data/LD/results_newdata/LD.trans.10.ld")
LD_trans_chr11 <- fread("./data/LD/results_newdata/LD.trans.11.ld")
LD_trans_chr12 <- fread("./data/LD/results_newdata/LD.trans.12.ld")
LD_trans_chr13 <- fread("./data/LD/results_newdata/LD.trans.13.ld")
LD_trans_chr14 <- fread("./data/LD/results_newdata/LD.trans.14.ld")
LD_trans_chr15 <- fread("./data/LD/results_newdata/LD.trans.15.ld")
LD_trans_chr16 <- fread("./data/LD/results_newdata/LD.trans.16.ld")
LD_trans_chr17 <- fread("./data/LD/results_newdata/LD.trans.17.ld")
LD_trans_chr18 <- fread("./data/LD/results_newdata/LD.trans.18.ld")
LD_trans_chr19 <- fread("./data/LD/results_newdata/LD.trans.19.ld")
LD_trans_chr20 <- fread("./data/LD/results_newdata/LD.trans.20.ld")
LD_trans_chr21 <- fread("./data/LD/results_newdata/LD.trans.21.ld")
LD_trans_chr22 <- fread("./data/LD/results_newdata/LD.trans.22.ld")
LD_trans_res <- rbind.data.frame(LD_trans_chr1, LD_trans_chr2, LD_trans_chr3, LD_trans_chr4,
LD_trans_chr5, LD_trans_chr6, LD_trans_chr7, LD_trans_chr8,
LD_trans_chr9, LD_trans_chr10, LD_trans_chr11, LD_trans_chr12,
LD_trans_chr13, LD_trans_chr14, LD_trans_chr15, LD_trans_chr16,
LD_trans_chr17, LD_trans_chr18, LD_trans_chr19, LD_trans_chr20,
LD_trans_chr21, LD_trans_chr22)
LD_trans_res <- rbind.data.frame(LD_trans_chr6, LD_trans_chr7, LD_trans_chr12,
LD_trans_chr16, LD_trans_chr20)# %>%
# filter(., SNP_A != SNP_B)
rm(LD_trans_chr1, LD_trans_chr2, LD_trans_chr3, LD_trans_chr4,
LD_trans_chr5, LD_trans_chr6, LD_trans_chr7, LD_trans_chr8,
LD_trans_chr9, LD_trans_chr10, LD_trans_chr11, LD_trans_chr12,
LD_trans_chr13, LD_trans_chr14, LD_trans_chr15, LD_trans_chr16,
LD_trans_chr17, LD_trans_chr18, LD_trans_chr19, LD_trans_chr20,
LD_trans_chr21, LD_trans_chr22)
# Supplementary Data
#fwrite(LD_cis_res, file = "./data/LD/LD_ciseQTL.txt")
#fwrite(LD_trans_res, file = "./data/LD/LD_transeQTL.txt")
SNPlist_lead_ciseQTL <- eQTLs_cis$SNP %>%
unique() %>%
as.data.frame()
SNPlist_lead_transeQTL <- eQTLs_trans$SNP %>%
unique() %>%
as.data.frame()
SNPlist_EA_clumped <- clump_res$SNP %>%
as.data.frame()
if(!dir.exists(paste0("./data/SuppData/eQTL/"))){
dir.create(paste0("./data/SuppData/eQTL/"))
}
list_eQTL <- list("Lead eQTLs cis" = eQTLs_cis,
"SNPlist lead ciseQTL" = SNPlist_lead_ciseQTL,
"Lead eQTLs trans" = eQTLs_trans,
"SNPlist lead transeQTL" = SNPlist_lead_transeQTL,
"Clumped EA GWAS" = clump_res,
"SNPlist lead EA GWAS clumped" = SNPlist_EA_clumped,
"cis eQTLs in LD" = LD_cis_res,
"trans eQTLs in LD" = LD_trans_res)
write.xlsx(list_eQTL, file = paste0("./data/SuppData/eQTL/SuppData_eQTL.xlsx"),
col.names = TRUE, row.names = FALSE,
overwrite = TRUE)