compare obtained SNP

compare_snps.R

+## load new and old SNP positions
+## create new SNP ID
+## compare SNP identified with both methods, see if overlap
+
+setwd("~/Documents/project_SEACONNECT/seaConnect--annotationVariant/annotationvariant/")
+
+# read in SNP positions
+tbl_dip_cds    <- read.table("diplodus/diplodus_CDS_pos.txt")
+tbl_dip_cdsns  <- read.table("diplodus/diplodus_CDS_nonsynonymous_pos.txt")
+tbl_dip_pca    <- read.table("diplodus/diplodus_pcadapt_pos.txt")
+tbl_dip_pcaupns <- read.table("../../seaConnect--radFishComp/200_genome_BLAST/04-filter_uniprot/diplodus_CDS_uniprot_nonsynonymous.tsv")
+
+tbl_mul_cds   <- read.table("mullus/mullus_CDS_pos.txt")
+tbl_mul_cdsns <- read.table("mullus/mullus_CDS_nonsynonymous_pos.txt")
+tbl_mul_pca   <- read.table("mullus/mullus_pcadapt_pos.txt")
+
+# create new ID
+dip_cds    <- paste(tbl_dip_cds$V1, tbl_dip_cds$V2, sep = "_")
+dip_pca    <- paste(tbl_dip_pca$V1, tbl_dip_pca$V2, sep = "_")
+dip_cdsns  <- paste(tbl_dip_cdsns$V1, tbl_dip_cdsns$V2, sep = "_")
+dip_pcaupns<- paste(tbl_dip_pcaupns$V1, tbl_dip_pcaupns$V2, sep = "_")
+
+mul_cds    <- paste(tbl_mul_cds$V1, tbl_mul_cds$V2, sep = "_")
+mul_pca    <- paste(tbl_mul_pca$V1, tbl_mul_pca$V2, sep = "_")
+mul_cdsns  <- paste(tbl_mul_cdsns$V1, tbl_mul_cdsns$V2, sep = "_")
+
+# compare obtained SNPs with both methods
+dip_cdsXpca <- intersect(dip_cds,dip_pca)
+dip_cdsnsXpca <- intersect(dip_cds_ns,dip_pca)
+dip_cdsXpcaXcdsns <- intersect(intersect(dip_cds, dip_pca), dip_cds_ns)
+
+dip_A <- setdiff(setdiff(dip_cds, dip_cds_ns), dip_pca)
+dip_B <- setdiff(setdiff(dip_cds_ns, dip_pca), dip_cds)
+dip_C <- setdiff(dip_pca, dip_cds)
+dip_AB <- setdiff(intersect(dip_cds, dip_cds_ns), dip_pca)
+dip_AC <- setdiff(intersect(dip_cds, dip_pca), dip_cds_ns)
+dip_BC <- setdiff(intersect(dip_cds_ns, dip_pca), dip_cds)
+dip_ABC <- intersect(intersect(dip_cds, dip_pca), dip_cds_ns)
+
+dip_plusplus <- intersect(dip_cds_ns, dip_pca_cds_up_ns)
+
+mul_cdsXpca <- intersect(mul_cds, mul_pca)
+mul_cdsnsXpca <- intersect(mul_cds_ns, mul_pca)
+mul_cdsXpcaXcdsns <- intersect(intersect(mul_cds, mul_pca), mul_cds_ns)
+
+mul_A <- setdiff(setdiff(mul_cds, mul_cds_ns), mul_pca)
+mul_B <- setdiff(setdiff(mul_cds_ns, mul_pca), mul_cds)
+mul_C <- setdiff(mul_pca, mul_cds)
+mul_AB <- setdiff(intersect(mul_cds, mul_cds_ns), mul_pca)
+mul_AC <- setdiff(intersect(mul_cds, mul_pca), mul_cds_ns)
+mul_BC <- setdiff(intersect(mul_cds_ns, mul_pca), mul_cds)
+mul_ABC <- intersect(intersect(mul_cds, mul_pca), mul_cds_ns)
+
+## euler diagrams
+library(eulerr)
+dip_fit <- euler(c("A" = length(dip_cds)-length(dip_cdsXpca),
+                   "B" = length(dip_pca)-length(dip_cdsXpca),
+                   "A&B" = length(dip_cdsXpca)))
+plot(dip_fit, quantities = TRUE, labels = TRUE)
+
+dip_fit2 <- euler(c("CDS" = length(dip_A),
+                    "CDS_NS" = length(dip_B),
+                    "PCA" = length(dip_C),
+                    "CDS&CDS_NS" = length(dip_AB),
+                    "CDS&PCA" = length(dip_AC),
+                    "CDS_NS&PCA" = length(dip_BC),
+                    "CDS&CDS_NS&PCA" = length(dip_ABC)))
+plot(dip_fit2, quantities = TRUE, labels = TRUE)
+
+
+mul_fit <- euler(c("A" = length(mul_cds_id)-length(mul_comm),
+                   "B" = length(mul_pca_id)-length(mul_comm),
+                   "A&B" = length(mul_comm)))
+plot(mul_fit, quantities = TRUE, labels = TRUE)
+
+mul_fit2 <- euler(c("CDS" = length(mul_A),
+                    "CDS_NS" = length(mul_B),
+                    "PCA" = length(mul_C),
+                    "CDS&CDS_NS" = length(mul_AB),
+                    "CDS&PCA" = length(mul_AC),
+                    "CDS_NS&PCA" = length(mul_BC),
+                    "CDS&CDS_NS&PCA" = length(mul_ABC)))
+plot(mul_fit2, quantities = TRUE, labels = TRUE)

compare_snps.sh

+# compare lists of SNP 
+
+## Diplodus
+# get CDS positions
+grep -v "^##" "diplodus/diplodus_CDS.vcf" | cut -f1-2 | sed '1d' > "diplodus/diplodus_CDS_pos.txt"
+# get pcadapt outlier positions
+grep -v "^##" "../../seaConnect--dataPrep/04-finalPrep/01-Diplodus/dip_adaptive_413.vcf" | cut -f1-2 | sed '1d' > "diplodus/diplodus_pcadapt_pos.txt"
+
+## Mullus
+# get CDS positions
+grep -v "^##" "mullus/mullus_CDS.vcf" | cut -f1-2 | sed '1d' > "mullus/mullus_CDS_pos.txt"
+# get pcadapt outlier positions
+grep -v "^##" "../../seaConnect--dataPrep/04-finalPrep/02-Mullus/mul_adaptive_291.vcf" | cut -f1-2 | sed '1d' > "mullus/mullus_pcadapt_pos.txt"
+