-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathcharr_CNV_rep_compare.R
389 lines (314 loc) · 22.9 KB
/
charr_CNV_rep_compare.R
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
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
setwd("~/Desktop/Charr_Reanalysis/")
library(data.table)
library(tidyverse)
library(data.table)
#Identifying and removing CNVs, repetitive regions, then re-running popgen analyses
#Charr_LG_Chrom_Conversion
CHar_LG_Chrom_Conversion <- read.delim("~/Desktop/Charr_Final_Scripts_Data/CHar_LG_Chrom_Conversion.txt", stringsAsFactors=FALSE, header = F)
colnames(CHar_LG_Chrom_Conversion) <- c("LG", "CM_Chrom", "NC_Chrom")
#CNVNATOR
dark_cnvnator_edited <- read.delim("~/Desktop/Charr_Reanalysis/dark_cnvnator_edited.tsv", header=FALSE)
colnames(dark_cnvnator_edited) <- c("Type", "CM_Chrom", "BP", "Pos2", "Size", "Normalized_RD",
"pval1", "pval2","pval3", "pval4", "q")
pale_cnvnator_edited <- read.delim("~/Desktop/Charr_Reanalysis/pale_cnvnator_edited.tsv", header=FALSE)
colnames(pale_cnvnator_edited) <- c("Type", "CM_Chrom", "BP", "Pos2", "Size", "Normalized_RD",
"pval1", "pval2","pval3", "pval4", "q")
pale_cnvnator_bed<- data.frame(cbind(pale_cnvnator_edited$CM_Chrom, pale_cnvnator_edited$BP, pale_cnvnator_edited$Pos2))
write.table(pale_cnvnator_bed, "pale_cnvnator.bed", col.names = F, row.names = F, sep = "\t", quote = F)
dark_cnvnator_bed<- data.frame(cbind(dark_cnvnator_edited$CM_Chrom, dark_cnvnator_edited$BP, dark_cnvnator_edited$Pos2))
write.table(dark_cnvnator_bed, "dark_cnvnator.bed", col.names = F, row.names = F, sep = "\t", quote = F)
#filter for comparison with SI outliers
dark_cnvnator_filtered <- dark_cnvnator_edited[which(dark_cnvnator_edited$q > 0.5),]
pale_cnvnator_filtered <- pale_cnvnator_edited[which(pale_cnvnator_edited$q > 0.5),]
pale_cnvnator_filtered_bed<- data.frame(cbind(pale_cnvnator_filtered$CM_Chrom, pale_cnvnator_filtered$BP, pale_cnvnator_filtered$Pos2))
write.table(pale_cnvnator_filtered_bed, "pale_cnvnator_filter.bed", col.names = F, row.names = F, sep = "\t", quote = F)
dark_cnvnator_filtered_bed<- data.frame(cbind(dark_cnvnator_filtered$CM_Chrom, dark_cnvnator_filtered$BP, dark_cnvnator_filtered$Pos2))
write.table(dark_cnvnator_filtered_bed, "dark_cnvnator_filter.bed", col.names = F, row.names = F, sep = "\t", quote = F)
#VST Signal intensity OL
GDL_pale_GDL_dark_CNV_OL <- read.delim("~/Desktop/Charr_Reanalysis/RDA_and_VST_OL.txt", header=T, stringsAsFactors=FALSE)
colnames(GDL_pale_GDL_dark_CNV_OL)[3] <- "BP"
CHar_LG_Chrom_Conversion_VST <- read.table("CHar_LG_Chrom_Conversion_VST.txt", quote="\"", comment.char="", stringsAsFactors=FALSE)
colnames(CHar_LG_Chrom_Conversion_VST) <- c("LG", "LG_alt", "CM_Chrom", "NC_Chrom")
GDL_VST <- read.delim("~/Desktop/Charr_Reanalysis/GDL_dark_rn_GDL_pale_rn.Vst.txt", header=FALSE, stringsAsFactors=FALSE)
colnames(GDL_VST) <- c("SNP", "LG_alt", "BP", "C", "VST")
colnames(CHar_LG_Chrom_Conversion_VST) <- c("LG", "LG_alt", "CM_Chrom", "NC_Chrom")
GDL_VST <- inner_join(GDL_VST, CHar_LG_Chrom_Conversion_VST)
GDL_VST_OL <- inner_join(GDL_pale_GDL_dark_CNV_OL, GDL_VST)
VSTANDRDAOL <- fread("Charr_VSTANDRDAOL.bed", data.table = F)
colnames(VSTANDRDAOL) <- c("NC_Chrom", "Pos1", "Pos2")
VSTANDRDAOL <- inner_join(VSTANDRDAOL,CHar_LG_Chrom_Conversion)
#Removing ALL CNV and repetitive regions.
#Repeatmasker
Charr_repeat <- fread("Charr_repeatregions_simple.txt", stringsAsFactors = F, data.table = F)
Charr_repeat <- inner_join(CHar_LG_Chrom_Conversion, Charr_repeat)
Charr_repeat_bed <- data.frame(cbind(Charr_repeat$CM_Chrom, Charr_repeat$Pos1, Charr_repeat$Pos2))
colnames(Charr_repeat_bed) <- c("CM_Chrom", "Pos1", "Pos2")
colnames(dark_cnvnator_bed) <- c("CM_Chrom", "Pos1", "Pos2")
colnames(pale_cnvnator_bed) <- c("CM_Chrom", "Pos1", "Pos2")
VSTANDRDAOL <- data.frame(cbind(VSTANDRDAOL[5],VSTANDRDAOL[2:3]))
colnames(VSTANDRDAOL) <- c("CM_Chrom", "Pos1", "Pos2")
All_potential_reps <- data.frame(rbind(Charr_repeat_bed, dark_cnvnator_bed, pale_cnvnator_bed, VSTANDRDAOL))
All_potential_reps$Pos1 <- as.numeric(All_potential_reps$Pos1)
All_potential_reps$Pos2 <- as.numeric(All_potential_reps$Pos2)
All_potential_reps <- All_potential_reps %>% arrange(CM_Chrom, Pos1)
write.table(All_potential_reps, "AP_reps.bed", sep = "\t", col.names = F, row.names = F, quote = F)
Charr_map <- fread("Charrchip_Poly_GDL_comp.map", data.table = F, stringsAsFactors = F)
colnames(Charr_map)[1] <- "NC_Chrom"
Charr_map_CM <- inner_join(Charr_map, CHar_LG_Chrom_Conversion)
write.table(cbind(Charr_map_CM$CM_Chrom, Charr_map_CM[2:4]), "Charrchip_Poly_GDL_comp_CM.map",
sep = "\t", col.names = F, row.names = F, quote = F)
###Sort it out
system("~/Desktop/Software/plink_mac_20200219/plink --ped Charrchip_Poly_GDL_comp.ped --map Charrchip_Poly_GDL_comp_CM.map --recode vcf --allow-extra-chr --out Charrchip_Poly_GDL_comp")
system("bedtools merge -i AP_reps.bed > AP_reps_merged.bed")
system("bedtools intersect -a Charrchip_Poly_GDL_comp.vcf -b AP_rep_merge.bed -v > Charr_Poly_GDL_comp_norep.vcf")
AP_reps_merged <- read.delim("AP_reps_merged.bed", stringsAsFactors = F, header = F)
AP_reps_merged$size <- AP_reps_merged$V3 - AP_reps_merged$V2
colnames(AP_reps_merged)[1] <- "CM_Chrom"
AP_reps_merged <- inner_join(AP_reps_merged, CHar_LG_Chrom_Conversion)
ggplot() + geom_density(data = AP_reps_merged, aes(x = size)) + theme_classic()
max(AP_reps_merged$size)
#"awk '{OFS="\t"}{print $1,$2}' Charr_Poly_GDL_comp_norep.vcf > Charr_norep.tsv probably there's a nice way to do this in R terminal but just open a command line terminal
Charrchip_norep <- read.delim("Charr_norep.tsv", header = F)
colnames(Charrchip_norep) <- c("CM_Chrom", "V4")
Charrchip_norep <- inner_join(Charrchip_norep, Charr_map_CM)
write.table(Charrchip_norep$V2, "Charrchip_norep_SNPS.txt", sep = "\t",
col.names = F, row.names = F, quote = F)
system("~/Desktop/Software/plink_mac_20200219/plink --file Charrchip_Poly_GDL_comp --recode --maf 0.05 --extract Charrchip_norep_SNPS.txt --allow-extra-chr --out Charrchip_Poly_GDL_comp_norep")
##Check how this performs with quick outlier test PCA etc.
library(pcadapt)
CHARR_GANDER <- read.pcadapt("Charrchip_Poly_GDL_comp_norep.ped", type = "ped")
PCs_GDL <- pcadapt(CHARR_GANDER, K=1, method="mahalanobis", min.maf = 0.01)
PCs_GDL$singular.values ^ 2
plot(PCs_GDL,option="scores")
(PCs_GDL$singular.values)^2
GDL_IDs <-system("awk '{print $2}' Charrchip_Poly_GDL_comp_norep.ped ", intern = T)
GDL_PC_SCORES <- as.data.frame(cbind(GDL_IDs, PCs_GDL$scores))
GDL_PHENO <- read.delim("GDL_PHENO2.txt", header = T, stringsAsFactors = F)
GDL_PC_SCORES <- merge(GDL_PHENO, GDL_PC_SCORES, by.x = "CHIP_ID", by.y = "GDL_IDs")
GDL_PC_SCORES$V2 <- as.numeric(as.character(GDL_PC_SCORES$V2))
##for K=2
##GDL_PC_SCORES$V3 <- as.numeric(as.character(GDL_PC_SCORES$V3))
plot(PCs_GDL, option="scores")
#Nicer Plot
colnames(GDL_PC_SCORES) = c("CHIP_ID","Jar_ID","Phenotype","Year","PC1")
##for K=2
###ggplot(GDL_PC_SCORES, aes(x=PC1, y = PC2, col=Phenotype, shape=Year)) + geom_point() + xlab("PC1") + ylab("PC2") + scale_color_manual(values = c("antiquewhite4","burlywood")) + theme_classic()
colnames(GDL_PC_SCORES) = c("CHIP_ID","Jar_ID","Phenotype","Year","PC1")
ggplot(GDL_PC_SCORES, aes(x=PC1, fill=Phenotype)) + geom_density() + xlab("PC1") + scale_fill_manual(values = c("antiquewhite4","burlywood")) + theme_classic()
MAPPOS <- read.delim2("Charrchip_Poly_GDL_comp_norep.map", header = F)
colnames(MAPPOS) <- c("Chrom", "SNP", "CM", "BP")
PVALS <- PCs_GDL$pvalues
PCMAP <- as.data.frame(cbind(MAPPOS, PVALS))
library(qvalue)
qval <- qvalue(PCs_GDL$pvalues)$qvalues
alpha <- 0.05
outliers <- which(qval<alpha)
Outliers_CHARR_norep <- PCMAP[outliers,]
write.table(Outliers_CHARR_norep, "PCAdapt_CHARRGDL_Poly_Outliers_K1_Q05_noreps.txt", sep = "\t", quote = FALSE, col.names = TRUE, row.names = FALSE)
inner_join(cnvnator_filtered_distinct_genes_bed_NC, cnvnator_filtered_distinct_genes_NC_old)
cnvnator_filtered_distinct_genes_bed_NC$V2 <- as.integer(cnvnator_filtered_distinct_genes_bed_NC$V2)
cnvnator_filtered_distinct_genes_bed_NC$V3 <- as.integer(cnvnator_filtered_distinct_genes_bed_NC$V3)
colnames(cnvnator_filtered_distinct_genes_bed_NC) <- c("V1", "V2", "V3", "Symbol")
#just neutral LE SNPS
system("~/Desktop/Software/plink_mac_20200219/plink --file Charchip_GDL_Neut_Poly_LE --recode --maf 0.05 --extract Charrchip_norep_SNPS.txt --allow-extra-chr --out Charrchip_Poly_GDL_Neut_Poly_norep")
library(pcadapt)
CHARR_GANDER <- read.pcadapt("Charrchip_Poly_GDL_Neut_Poly_norep.ped", type = "ped")
PCs_GDL <- pcadapt(CHARR_GANDER, K=1, method="mahalanobis", min.maf = 0.01)
PCs_GDL$singular.values ^ 2
plot(PCs_GDL,option="scores")
(PCs_GDL$singular.values)^2
GDL_IDs <-system("awk '{print $2}' Charrchip_Poly_GDL_Neut_Poly_norep.ped ", intern = T)
GDL_PC_SCORES <- as.data.frame(cbind(GDL_IDs, PCs_GDL$scores))
GDL_PHENO <- read.delim("GDL_PHENO2.txt", header = T, stringsAsFactors = F)
GDL_PC_SCORES <- merge(GDL_PHENO, GDL_PC_SCORES, by.x = "CHIP_ID", by.y = "GDL_IDs")
GDL_PC_SCORES$V2 <- as.numeric(as.character(GDL_PC_SCORES$V2))
##for K=2
##GDL_PC_SCORES$V3 <- as.numeric(as.character(GDL_PC_SCORES$V3))
plot(PCs_GDL, option="scores")
#Nicer Plot
colnames(GDL_PC_SCORES) = c("CHIP_ID","Jar_ID","Phenotype","Year","PC1")
##for K=2
###ggplot(GDL_PC_SCORES, aes(x=PC1, y = PC2, col=Phenotype, shape=Year)) + geom_point() + xlab("PC1") + ylab("PC2") + scale_color_manual(values = c("antiquewhite4","burlywood")) + theme_classic()
colnames(GDL_PC_SCORES) = c("CHIP_ID","Jar_ID","Phenotype","Year","PC1")
ggplot(GDL_PC_SCORES, aes(x=PC1, fill=Phenotype)) + geom_density() + xlab("PC1") + scale_fill_manual(values = c("antiquewhite4","burlywood")) + theme_classic()
library(ggman)
ggman(PCMAP, chrom = "Chrom", pvalue = "PVALS", snp = "SNP", bp="BP", pointSize = 1, title = "CHARR", xlabel = "Chromosome", sigLine = -log10(max(Outliers_CHARR$PVALS)),ymax = 300) + theme_classic()
#PCangsd selscan
library(RcppCNPy)
library(qvalue)
S <- npyLoad("PC_charr_mq30.selection.npy") # Reads results from selection scan
sites <- fread("PC_charr_mq30.sites", data.table = F, stringsAsFactors = F, header = F)
pcangsd_sel <- cbind(S, sites)
colnames(pcangsd_sel) <- c("PC_S","CM_Chrom", "BP")
write.table((cbind(sites$V1, sites$V2, sites$V2 + 1)), "pcangsd_charr_sites.bed", sep = "\t", quote = F, row.names = F, col.names = F)
system("bedtools intersect -a pcangsd_charr_sites.bed -b AP_rep_merge.bed -v > pcangsd_sites_norep_jr.tsv")
#PCA and admixture with filtered
setwd("~/Desktop/Tony/Charr/")
library(RcppCNPy)
library(ggplot2)
library(dplyr)
library(tidyverse)
C <- read.delim("PC_charr_mq30_norepmaf05.cov", sep = "", header = F)
PCA <- eigen(C)
PCA_scores <- data.frame(PCA$vectors[,1:2], stringsAsFactors = F)
plot(PCA_scores$X1, PCA_scores$X2, )
PCA_scores$MORPH <- c(rep("Pelagic", 10), rep("Deep-water", 10))
ggplot(data = PCA_scores) + geom_density(aes(x = X1, fill = MORPH)) + theme_classic() + scale_fill_manual(values = c("burlywood", "antiquewhite4"))
eigenvalues <- PCA$values
eigenvalues[1]/sum(eigenvalues)
Admix <- data.frame(npyLoad("PC_charr_mq30_norepmaf05.admix.Q.npy"), stringsAsFactors = F)
Admix$MORPH <- PCA_scores$MORPH
Admix$ID <- as.numeric(rep(1:20))
colnames(Admix)[1:2] <- c("K1", "K2")
plot_data <- Admix %>%
gather('K', 'ADMIX', K1:K2)
ggplot(plot_data, aes(ID, ADMIX, fill = K)) +
geom_col() + theme_classic()
#check outlier overlap
CHar_LG_Chrom_Conversion <- read.delim("~/Desktop/Charr_Final_Scripts_Data/CHar_LG_Chrom_Conversion.txt", stringsAsFactors=FALSE, header = F)
colnames(CHar_LG_Chrom_Conversion) <- c("LG", "CM_Chrom", "NC_Chrom")
S <- npyLoad("PC_charr_mq30_norepmaf05.selection.npy") # Reads results from selection scan
sites <- fread("PC_charr_mq30_norepmaf05.sites", data.table = F, stringsAsFactors = F, header = F)
pcangsd_sel <- cbind(S, sites)
colnames(pcangsd_sel) <- c("PC_S","CM_Chrom", "BP")
pcangsd_sel <- inner_join(pcangsd_sel, CHar_LG_Chrom_Conversion)
pcangsd_sel_maxes <- pcangsd_sel %>%
group_by(LG) %>%
filter(BP == max(BP))
pcangsd_sel_maxes <- data.frame(pcangsd_sel_maxes, stringsAsFactors = F)
pcangsd_sel_maxes$BP <- as.integer(pcangsd_sel_maxes$BP)
pcangsd_sel_maxes$BP <- pcangsd_sel_maxes$BP + 2000
pcangsd_sel_dummy <- rbind(pcangsd_sel_maxes, pcangsd_sel)
pcangsd_sel_1kwin <- winScan(x = pcangsd_sel_dummy, groups = "LG", position = "BP", win_size = 1000, win_step = 1000, values = "PC_S", funs = "mean")
pcangsd_sel_1kwin <- pcangsd_sel_1kwin[which(pcangsd_sel_1kwin$PC_S_n > 0),]
pcangsd_sel_1kwin$BP <- pcangsd_sel_1kwin$win_mid
#write out so that windows don't need to be recalculated (should have done this much earlier...)
write.table(pcangsd_sel_1kwin, "pcangsd_sel_1kwin.txt", col.names = T, sep = "\t", row.names = F, quote = F)
pcangsd_sel_1kwin <- fread("pcangsd_sel_1kwin.txt", data.table = F, stringsAsFactors = F)
pcangsd_sel_1k_99OL<- pcangsd_sel_1kwin[which(pcangsd_sel_1kwin$PC_S_mean > quantile(pcangsd_sel_1kwin$PC_S_mean, 0.99, na.rm=T)),]
pcangsd_sel_1k_99OL$BP <- pcangsd_sel_1k_99OL$win_mid
pcangsd_1kOL_LGBP<- data.frame(cbind("LG" = pcangsd_sel_1k_99OL$LG, "BP" = pcangsd_sel_1k_99OL$BP), stringsAsFactors = F)
pcangsd_1kOL_LGBP$BP<- as.numeric(pcangsd_1kOL_LGBP$BP)
ALL_WG_OL_combo <- read.delim("Charr_WGOL_FST_and_PCA_OL99.bed", header = F)
colnames(ALL_WG_OL_combo) <- c("CM_Chrom", "BP", "BPplsuone")
combined <- inner_join(ALL_WG_OL_combo, pcangsd_1kOL_LGBP)
#Also redo PCA output real quick for a nice density plot
C <- read.delim("PC_charr_mq30.cov", sep = "", header = F)
PCA <- eigen(C)
PCA_scores <- data.frame(PCA$vectors[,1:2], stringsAsFactors = F)
plot(PCA_scores$X1, PCA_scores$X2, )
PCA_scores$MORPH <- c(rep("Pelagic", 10), rep("Deep-water", 10))
ggplot(data = PCA_scores) + geom_density(aes(x = X1, fill = MORPH)) + theme_classic() + scale_fill_manual(values = c("burlywood", "antiquewhite4"))
eigenvalues <- PCA$values
eigenvalues[1]/sum(eigenvalues)
###Identifying distinct CNVs
#Import annotation
charr_genome_annotation <- read.csv("~/Desktop/Charr_Reanalysis/charr_genome_annotation.csv")
colnames(charr_genome_annotation)[11] <- "LG"
charr_genome_annotation <- inner_join(charr_genome_annotation, CHar_LG_Chrom_Conversion)
write.table(cbind(charr_genome_annotation$CM_Chrom, charr_genome_annotation$start_position_on_the_genomic_accession, charr_genome_annotation$end_position_on_the_genomic_accession, charr_genome_annotation$Symbol),
"charr_genes.bed", sep = "\t", quote = F, col.names = F, row.names = F)
system("bedtools intersect -a charr_genes.bed -b dark_cnvnator_filter.bed -wb > dark_cnvnator_charrgenes.bed")
system("bedtools intersect -a charr_genes.bed -b pale_cnvnator_filter.bed -wb > pale_cnvnator_charrgenes.bed")
system("bedtools intersect -a charr_genes.bed -b Charr_VSTANDRDAOL.bed -wb > RDAVST_charrgenes.bed")
#import overlap
dark_genes_cnvnator <- read.delim("~/Desktop/Charr_Reanalysis/dark_cnvnator_charrgenes.bed", header = F)
colnames(dark_genes_cnvnator)<- c("CM_Chrom", "OL_start", "OL_stop", "Symbol", "Chrom2", "BP","Pos2")
dark_genes_cnvnator <- inner_join(dark_genes_cnvnator, dark_cnvnator_edited, by = c("CM_Chrom", "BP"))
dark_genes_cnvnator$morph <- "dark"
dark_genes_cnvnator$method <- "cnvnator"
dark_genes_cnvnator_unique <- unique(dark_genes_cnvnator$Symbol)
#import overlap
pale_genes_cnvnator <- read.delim("~/Desktop/Charr_Reanalysis/pale_cnvnator_charrgenes.bed", header = F)
colnames(pale_genes_cnvnator)<- c("CM_Chrom", "OL_start", "OL_stop", "Symbol", "Chrom2", "BP","Pos2")
pale_genes_cnvnator <- inner_join(pale_genes_cnvnator, pale_cnvnator_edited, by = c("CM_Chrom", "BP"))
pale_genes_cnvnator$morph <- "pale"
pale_genes_cnvnator$method <- "cnvnator"
pale_genes_cnvnator_unique <- unique(pale_genes_cnvnator$Symbol)
dark_CNVnator_distinct <- anti_join(dark_genes_cnvnator, pale_genes_cnvnator, by = c("Symbol"))
pale_CNVnator_distinct <- anti_join( pale_genes_cnvnator, dark_genes_cnvnator, by = c("Symbol"))
pale_CNVnator_distinct_annot <- inner_join(pale_CNVnator_distinct, charr_genome_annotation, by = "Symbol")
dark_CNVnator_distinct_annot <- inner_join(dark_CNVnator_distinct, charr_genome_annotation, by = "Symbol")
dark_CNVnator_distinct_annot_short <- dark_CNVnator_distinct_annot %>% select(c("CM_Chrom.x", "Symbol", "description", "morph", "BP" ,"Pos2.x","Type", "Size","q", "pval1", "pval2"))
pale_CNVnator_distinct_annot_short <- pale_CNVnator_distinct_annot %>% select(c("CM_Chrom.x", "Symbol", "description","morph", "BP", "Pos2.x","Type", "Size","q", "pval1", "pval2"))
distinct_annot_short <- rbind(pale_CNVnator_distinct_annot_short, dark_CNVnator_distinct_annot_short)
write.table(distinct_annot_short, "distinct_CNVnator_annotated.txt", col.names = T, row.names = F, quote = F, sep = "\t")
#Overlap AND VST info
write.table(cbind(GDL_VST_OL$CM_Chrom, GDL_VST_OL$BP, GDL_VST_OL$BP+1, GDL_VST_OL$VST), "GDL_VSTOL.bed",
sep = "\t", col.names = F, row.names = F, quote = F)
VST_OL_genes <- read.table("VSTOL_gene_overlap")
colnames(VST_OL_genes) <- c("CM_Chrom", "BP", "BP2", "Symbol")
VST_OL_genes <- inner_join(VST_OL_genes, GDL_VST_OL)
VST_OL_genes_annot <- inner_join(VST_OL_genes, charr_genome_annotation, by = "Symbol")
dark_VST_WG_genes <- inner_join(dark_CNVnator_distinct_annot_short, VST_OL_genes, by = "Symbol")
pale_VST_WG_genes <- inner_join(pale_CNVnator_distinct_annot_short, VST_OL_genes, by = "Symbol")
anti_join(dark_VST_WG_genes, pale_VST_WG_genes, by = "Symbol")
anti_join(pale_VST_WG_genes, dark_VST_WG_genes, by = "Symbol")
inner_join(dark_VST_WG_genes, pale_VST_WG_genes, by = "Symbol")
VST_WG_genes<- rbind(pale_VST_WG_genes, dark_VST_WG_genes)
unique(VST_WG_genes$Symbol)
#Outlier region, fst, PCA comparison
paledark_fst <- read.delim("~/Desktop/Charr_Reanalysis/Old Charr files/Charr_Linux(1)/paledark.fst", header=FALSE)
colnames(paledark_fst) <- c("CM_Chrom", "BP", "SNPs", "Coverage_proportion", "mean_coverage", "pops_compared", "FST")
paledark_fst <- inner_join(CHar_LG_Chrom_Conversion, paledark_fst)
#Import chip map
Charrchip_map <- read.delim("~/Desktop/Charr_Reanalysis/Charrchip_Poly_GDL_comp.map", header=FALSE, stringsAsFactors=FALSE)
colnames(Charrchip_map) <- c("NC_Chrom", "SNP", "whatev", "BP")
CHIP_FST <- read.delim("~/Desktop/Charr_Reanalysis/FST_GDLCharr_diveRsity.txt", stringsAsFactors=FALSE)
CHIP_FST <- data.frame(cbind(CHIP_FST$loci, CHIP_FST$Fst_WC),stringsAsFactors = F)
colnames(CHIP_FST) <- c("SNP", "FST")
CHIP_FST <- inner_join(CHIP_FST, Charrchip_map)
CHIP_FST <- inner_join(CHIP_FST, CHar_LG_Chrom_Conversion)
CHIP_FST$FST <- as.numeric(CHIP_FST$FST)
CHIP_VST_WIN <- winScan(x = GDL_VST_OL_dummy, groups = "LG", position = "BP", win_size = 1000, win_step = 1000, values = "VST", funs = "mean")
CHIP_VST_WIN <- CHIP_VST_WIN[CHIP_VST_WIN$VST_n >0,]
CHIP_VST_WIN$BP <- CHIP_VST_WIN$win_mid
write.table(CHIP_VST_WIN, "CHIP_VST_WIN.txt", sep = "\t", quote = F, col.names = T, row.names = F)
CHIP_VST_WIN <- read.delim("CHIP_VST_WIN.txt", header = T)
VSTOL_FST <- inner_join(paledark_fst, CHIP_VST_WIN)
NOTVSTOL_FST <- anti_join(paledark_fst, CHIP_VST_WIN)
mean(NOTVSTOL_FST$FST)
mean(VSTOL_FST$FST)
mean(paledark_fst$FST)
wilcox.test(NOTVSTOL_FST$FST, VSTOL_FST$FST)
#FST and gene overlap of CNVs
pale_dark_fst_bed<- data.frame(cbind(paledark_fst$CM_Chrom, paledark_fst$BP , paledark_fst$BP + 1, paledark_fst$FST))
write.table(pale_dark_fst_bed, "paledark_fst.bed", col.names = F, row.names = F, sep = "\t", quote = F)
dark_cnvnator_filtered <- dark_cnvnator_edited[which(dark_cnvnator_edited$q > 0.5),]
pale_cnvnator_filtered <- pale_cnvnator_edited[which(pale_cnvnator_edited$q > 0.5),]
cnvnator_filtered <- rbind(dark_cnvnator_filtered, pale_cnvnator_filtered)
cnvnator_filtered <- distinct_at(cnvnator_filtered, vars(Type, CM_Chrom, BP, Pos2))
cnvnator_filtered <- inner_join(cnvnator_filtered, CHar_LG_Chrom_Conversion)
cnvnator_filtered_bed <- data.frame(cbind(cnvnator_filtered$CM_Chrom, cnvnator_filtered$BP, cnvnator_filtered$Pos2))
cnvnator_filtered_distinct <- rbind(dark_CNVnator_distinct, pale_CNVnator_distinct)
cnvnator_filtered_distinct <- inner_join(cnvnator_filtered_distinct, CHar_LG_Chrom_Conversion)
charr_genes_bed <- data.frame(cbind(charr_genome_annotation$CM_Chrom, charr_genome_annotation$start_position_on_the_genomic_accession, charr_genome_annotation$end_position_on_the_genomic_accession, charr_genome_annotation$Symbol))
cnvnator_filtered_distinct_genes_bed <- charr_genes_bed[charr_genes_bed$X4 %in% cnvnator_filtered_distinct$Symbol,]
colnames(cnvnator_filtered_distinct_genes_bed)[4] <- "Symbol"
write.table(cnvnator_filtered_distinct_genes_bed, "cnvnator_filtered_distinct_genes.bed", col.names = F, row.names = F, sep = "\t", quote = F )
charr_genes_bed_NC <- data.frame(cbind(charr_genome_annotation$NC_Chrom, charr_genome_annotation$start_position_on_the_genomic_accession, charr_genome_annotation$end_position_on_the_genomic_accession, charr_genome_annotation$Symbol))
cnvnator_filtered_distinct_genes_bed_NC <- charr_genes_bed_NC[charr_genes_bed_NC$X4 %in% cnvnator_filtered_distinct$Symbol,]
colnames(cnvnator_filtered_distinct_genes_bed_NC)[4] <- "Symbol"
write.table(cnvnator_filtered_distinct_genes_bed_NC, "cnvnator_filtered_distinct_genes_NC.bed", col.names = F, row.names = F, sep = "\t", quote = F )
write.table(pale_dark_fst_bed, "paledark_fst.bed", col.names = F, row.names = F, sep = "\t", quote = F)
system("bedtools intersect -a paledark_fst.bed -b cnvnator_filtered_distinct_genes.bed -wb > paledark_fst_cnvnator_filtered_distinctgenes")
Charr_WGOL99_bed <- read.table("Charr_WGOL_FST_and_PCA_OL99.bed")
colnames(Charr_WGOL99_bed)[1] <- "NC_Chrom"
Charr_WGOL99_bed<- inner_join(Charr_WGOL99_bed,CHar_LG_Chrom_Conversion )
write.table(cbind(Charr_WGOL99_bed$CM_Chrom, Charr_WGOL99_bed$V2, Charr_WGOL99_bed$V3), "Charr_WGOL_andPC_99_CM.bed", col.names = F, row.names = F, sep = "\t", quote = F)
system("bedtools intersect -a Charr_WGOL_andPC_99_CM.bed -b cnvnator_filtered_distinct_genes.bed -wb > WGOL99_cnvnator_filtered")
paledark_fst_cnvnator_filtered <- fread("paledark_fst_cnvnator_filtered_distinctgenes", data.table = F, stringsAsFactors = F)
paledark_WGOL99_cnvnator_filtered <- fread("WGOL99_cnvnator_filtered", data.table = F, stringsAsFactors = F)
colnames(paledark_WGOL99_cnvnator_filtered) <- c("CM_Chrom", "BP", "BPplusone", "CM_chrom_junior", "BP2", "BPsbackbaby", "Symbol")
paledark_WGOL99_cnvnator_filtered<- inner_join(paledark_fst, paledark_WGOL99_cnvnator_filtered)
paledark_WGOL99_cnvnator_filtered_annot <- inner_join(paledark_WGOL99_cnvnator_filtered, charr_genome_annotation, by = "Symbol")
colnames(paledark_fst_cnvnator_filtered) <- c("CM_Chrom", "BP", "BPplusone", "FST","CM_chrom_junior", "BP2", "BPsbackbaby", "Symbol")
paledark_fst_cnvnator_filtered_annot <- inner_join(paledark_fst_cnvnator_filtered, charr_genome_annotation, by = "Symbol" )
colnames(ALL_WG_OL_combo)[1] <- "NC_Chrom"
ALL_WG_OL_combo <- inner_join(ALL_WG_OL_combo, CHar_LG_Chrom_Conversion)
ALL_WG_OL_combo <- inner_join(ALL_WG_OL_combo, paledark_fst, by = c("CM_Chrom", "BP"))
ggplot() + geom_density(data =paledark_fst, aes(x = FST, colour = "Genome average")) +
geom_density(data =paledark_fst_cnvnator_filtered, aes(x = FST, colour = "CNVnator CNVs")) +
geom_density(data =Chip_OL, aes(x = FST, colour = "Chip FST OL")) +
geom_density(data =ALL_WG_OL_combo , aes(x = FST, colour = "CWG OL")) +
geom_density(data =VSTOL_FST, aes(x = FST, colour = "VST outliers")) + theme_classic() + geom_vline(xintercept = 0.11)