R/vcf2excel_jma_version.R
In itamuria/immunoeasy: Make Immuno Therapies An Easier Process
Defines functions
from_vcf2excel_somatica
from_vcf2excel_germinal
from_vcf2excel_germinal <- function(name_vcffile = "exome_pass_v011.vcf",
rdatafile = "20201125_vcf_MB14802_s11",save = TRUE)
{
# setwd("Exoma/EXOMA_EAA001_V300056632_L02/")
# dir()
# name_vcffile = "exome_pass_v011.vcf"
vcffile <- utils::read.table(name_vcffile)
vcffile$V9 <- as.character(vcffile$V9)
names9 <- strsplit(vcffile$V9,":")[[1]]
len9 <- length(names9)
col10 <- unlist(strsplit(as.character(vcffile$V10),":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
names(col10b) <- names9
col10b$AD <- as.character(col10b$AD)
col10b$PL <- as.character(col10b$PL)
sp2 <- strsplit(col10b$AD, ",")
AD1 <- unlist(lapply(sp2, `[[`, 1))
AD2 <- unlist(lapply(sp2, `[[`, 2))
sp3 <- strsplit(col10b$PL, ",")
PL1 <- unlist(lapply(sp3, `[[`, 1))
PL2 <- unlist(lapply(sp3, `[[`, 2))
PL3 <- unlist(lapply(sp3, `[[`, 3))
col10_fin <- cbind(col10b, AD1, AD2, PL1, PL2,PL3)
# Read header
d <- readLines(name_vcffile, n = 1000)
rm_lines <- grep("INFO=",d)
d <- d[rm_lines]
d <- gsub("##INFO=<ID=","",d)
sp2 <- strsplit(d, ",")
info_names <- unlist(lapply(sp2, `[[`, 1))
vcffile[,info_names] <- ""
# Funtzioa
vcffile$V8 <- as.character(vcffile$V8)
sp3 <- strsplit(vcffile$V8, ";")
locname <- function(x, info)
{
all_string <- x[grep(paste0("^",info,"="),x)]
value_only <- gsub(paste0(info,"="), "", all_string, )
value_only <- value_only[1]
# vcffile[h,info_names[g]] <- value_only[1]
if(length(value_only) == 0) value_only <- NA
return(value_only)
}
# Loop
for(g in 1:length(info_names))
{
print(paste0(g, "/", length(info_names)))
vcffile[,info_names[g]] <- unlist(lapply(sp3, locname, info = info_names[g]))
}
# un1 <- unlist(lapply(sp3, locname, info = info_names[g]))
# table(un1)
# Biltzen
dftot <- cbind(vcffile[,-c(8:10)],col10_fin)
names(dftot)[1:7] <- c("Chr","Pos","ID","Ref","Alt","QUAL","Filt")
numvar <- c("Pos","ID","DP","esp6500siv2_ea",
"SIFT_score","Polyphen2_HDIV_score","Polyphen2_HVAR_score","LRT_score",
"MutationTaster_score","MutationAssessor_score","FATHMM_score","PROVEAN_score",
"VEST3_score","CADD_raw","CADD_phred","DANN_score","fathmm-MKL_coding_score",
"MetaSVM_score","MetaLR_score","integrated_fitCons_score",
"integrated_confidence_value", "GERPpp_RS",
"phyloP7way_vertebrate","phyloP20way_mammalian","phastCons7way_vertebrate",
"phastCons20way_mammalian","SiPhy_29way_logOdds","ExAC_ALL","ExAC_AFR","ExAC_AMR",
"ExAC_EAS","ExAC_FIN","ExAC_NFE","ExAC_OTH","ExAC_SAS",
"DP","AD1","AD2","PL1",
"PL2","PL3")
for(q in numvar)
{
dftot[,q] <- as.numeric(as.character(dftot[,q]))
}
# for(q in c(8:23,31,seq(38,64,2),66:71,75,76,78:82))
# {
# dftot[,q] <- as.numeric(as.character(dftot[,q]))
# }
if(save)
{
save(dftot, file = paste0(rdatafile, ".RData"))
write.csv(dftot, file = paste0(rdatafile, ".csv"))
}
}
# Somaticas
from_vcf2excel_somatica <- function(name_vcffile = "exome_pass_v011.vcf",
rdatafile = "20201125_vcf_Ex77801_s10",save = TRUE)
{
# setwd("Exoma/EXOMA_EAA001_V300056632_L02/")
# dir()
# name_vcffile = "exome_pass_v011.vcf"
vcffile <- utils::read.table(name_vcffile)
vcffile$V9 <- as.character(vcffile$V9)
OBQRC <- grep("OBQRC",vcffile$V9)
PGT <- grep("PGT",vcffile$V9)
table(vcffile$V9)
vcffile$OBQRC <- ifelse(rownames(vcffile)%in%OBQRC,"OBQRC",NA)
vcffile$PGT <- ifelse(rownames(vcffile)%in%PGT,"PGT",NA)
vcffile$group <- 0
vcffile$group[vcffile$OBQRC == "OBQRC" & is.na(vcffile$PGT)] <- 1
vcffile$group[vcffile$OBQRC == "OBQRC" & vcffile$PGT == "PGT"] <- 2
vcffile$group[is.na(vcffile$OBQRC) & is.na(vcffile$PGT)] <- 3
vcffile$group[vcffile$PGT == "PGT" & is.na(vcffile$OBQRC)] <- 4
vcffile$ID <- 1:(nrow(vcffile))
table(vcffile$group)
name_group <- names(table(vcffile$group))
# Extract names
u1 <- unique(vcffile$V9[vcffile$OBQRC == "OBQRC" & vcffile$PGT == "PGT"])
# if(!is.na(u1))
# {
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10[vcffile$group==1])
# g1_11 <- as.character(vcffile$V11[vcffile$group==1])
id_1 <- vcffile$ID[vcffile$group==1]
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = 12,byrow = TRUE))
col10c <- cbind(col10b,rep(NA,nrow(col10b)),rep(NA,nrow(col10b)),rep(NA,nrow(col10b)))
names(col10c) <- names9
# GROUP 2
g2_10 <- as.character(vcffile$V10[vcffile$group==2])
id_2 <- vcffile$ID[vcffile$group==2]
col210 <- unlist(strsplit(g2_10,":"))
col210b <- data.frame(matrix(col210,ncol = 15,byrow = TRUE))
col210c <- col210b
names(col210c) <- names9
# GROUP 3
g3_10 <- as.character(vcffile$V10[vcffile$group==3])
id_3 <- vcffile$ID[vcffile$group==3]
col310 <- unlist(strsplit(g3_10,":"))
col310b <- data.frame(matrix(col310,ncol = 8,byrow = TRUE))
col310c <- cbind(col310b[,1:8],data.frame(matrix(NA, nrow = nrow(col310b),ncol = 7, byrow = TRUE)))
names(col310c) <- names9
# GROUP 4
g4_10 <- as.character(vcffile$V10[vcffile$group==4])
id_4 <- vcffile$ID[vcffile$group==4]
col410 <- unlist(strsplit(g4_10,":"))
col410b <- data.frame(matrix(col410,ncol = 11,byrow = TRUE))
col410c <- cbind(col410b[,1:8],data.frame(matrix(NA, nrow = nrow(col410b),ncol = 4, byrow = TRUE)),col410b[,9:11])
names(col410c) <- names9
id_t <- c(id_1,id_2,id_3,id_4)
dfcol <- rbind(col10c,col210c,col310c,col410c)
# dfcol3 <- rbind(col11c,col211c,col311c,col411c)
dfcol2 <- cbind(id_t,dfcol)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
# names(dfcol2)[13:23]<- paste0(names(dfcol2)[2:12],"_tum")
dfcol2$AD <- as.character(dfcol2$AD)
dfcol2$F1R2 <- as.character(dfcol2$F1R2)
dfcol2$F2R1 <- as.character(dfcol2$F2R1)
add <- strsplit(dfcol2$AD, ",")
nadd <- unlist(lapply(add, length))
ad1a <- as.numeric(unlist(lapply(add, `[[`, 1)))
ad1b <- as.numeric(unlist(lapply(add, `[[`, 2)))
ad <- data.frame(ad1a, ad1b, nadd)
names(ad) <- c("AD_ref","AD_alt", "AD_n")
F1R2d <- strsplit(dfcol2$F1R2, ",")
nF1R2 <- unlist(lapply(F1R2d, length))
F1R21a <- as.numeric(unlist(lapply(F1R2d, `[[`, 1)))
F1R21b <- as.numeric(unlist(lapply(F1R2d, `[[`, 2)))
F1R2 <- data.frame(F1R21a, F1R21b, nF1R2)
names(F1R2) <- c("F1R2_ref","F1R2_alt","F1R2_n")
F2R1d <- strsplit(dfcol2$F2R1, ",")
nF2R1 <- unlist(lapply(F2R1d, length))
F2R11a <- as.numeric(unlist(lapply(F2R1d, `[[`, 1)))
F2R11b <- as.numeric(unlist(lapply(F2R1d, `[[`, 2)))
F2R1 <- data.frame(F2R11a, F2R11b, nF2R1)
names(F2R1) <- c("F2R1_ref","F2R1_alt", "F2R1_n")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1,3)],ad,dfcol2[,c(4:6)],F1R2,dfcol2[ ,7],F2R1,dfcol2[,c(8:ncol(dfcol2))])
# Read header
d <- readLines(name_vcffile, n = 1000)
rm_lines <- grep("INFO=",d)
d <- d[rm_lines]
d <- gsub("##INFO=<ID=","",d)
sp2 <- strsplit(d, ",")
info_names <- unlist(lapply(sp2, `[[`, 1))
vcffile[,info_names] <- ""
# Funtzioa
vcffile$V8 <- as.character(vcffile$V8)
sp3 <- strsplit(vcffile$V8, ";")
locname <- function(x, info)
{
all_string <- x[grep(paste0("^",info,"="),x)]
value_only <- gsub(paste0(info,"="), "", all_string, )
value_only <- value_only[1]
# vcffile[h,info_names[g]] <- value_only[1]
if(length(value_only) == 0) value_only <- NA
return(value_only)
}
# Loop
for(g in 1:length(info_names))
{
print(paste0(g, "/", length(info_names)))
vcffile[,info_names[g]] <- unlist(lapply(sp3, locname, info = info_names[g]))
}
# un1 <- unlist(lapply(sp3, locname, info = info_names[g]))
# table(un1)
# Biltzen
dftot <- cbind(vcffile[,-c(8:10)],formatfin)
names(dftot)[1:7] <- c("Chr","Pos","ID","Ref","Alt","QUAL","Filt")
numvar <- c("Pos","group","ID","CONTQ","DP","ECNT","GERMQ","esp6500siv2_ea",
"SIFT_score","Polyphen2_HDIV_score","Polyphen2_HVAR_score","LRT_score",
"MutationTaster_score","MutationAssessor_score","FATHMM_score","PROVEAN_score",
"VEST3_score","CADD_raw","CADD_phred","DANN_score","fathmm-MKL_coding_score",
"MetaSVM_score","MetaLR_score","integrated_fitCons_score",
"integrated_confidence_value", "GERPpp_RS",
"phyloP7way_vertebrate","phyloP20way_mammalian","phastCons7way_vertebrate",
"phastCons20way_mammalian","SiPhy_29way_logOdds","ExAC_ALL","ExAC_AFR","ExAC_AMR",
"ExAC_EAS","ExAC_FIN","ExAC_NFE","ExAC_OTH","ExAC_SAS",
"AD_ref","AD_alt","AD_n","AF","DP","F1R2_ref","F1R2_alt","F1R2_n",
"F2R1_ref","F2R1_alt","F2R1_n",
"OBF","OBP","OBQ","OBQRC")
for(q in numvar)
{
dftot[,q] <- as.numeric(as.character(dftot[,q]))
}
if(save)
{
save(dftot, file = paste0(rdatafile, ".RData"))
write.csv(dftot, file = paste0(rdatafile, ".csv"))
}
}
itamuria/immunoeasy documentation built on Sept. 30, 2022, 5:53 a.m.
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Defines functions from_vcf2excel_somatica from_vcf2excel_germinal
from_vcf2excel_germinal <- function(name_vcffile = "exome_pass_v011.vcf",
rdatafile = "20201125_vcf_MB14802_s11",save = TRUE)
{
# setwd("Exoma/EXOMA_EAA001_V300056632_L02/")
# dir()
# name_vcffile = "exome_pass_v011.vcf"
vcffile <- utils::read.table(name_vcffile)
vcffile$V9 <- as.character(vcffile$V9)
names9 <- strsplit(vcffile$V9,":")[[1]]
len9 <- length(names9)
col10 <- unlist(strsplit(as.character(vcffile$V10),":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
names(col10b) <- names9
col10b$AD <- as.character(col10b$AD)
col10b$PL <- as.character(col10b$PL)
sp2 <- strsplit(col10b$AD, ",")
AD1 <- unlist(lapply(sp2, `[[`, 1))
AD2 <- unlist(lapply(sp2, `[[`, 2))
sp3 <- strsplit(col10b$PL, ",")
PL1 <- unlist(lapply(sp3, `[[`, 1))
PL2 <- unlist(lapply(sp3, `[[`, 2))
PL3 <- unlist(lapply(sp3, `[[`, 3))
col10_fin <- cbind(col10b, AD1, AD2, PL1, PL2,PL3)
# Read header
d <- readLines(name_vcffile, n = 1000)
rm_lines <- grep("INFO=",d)
d <- d[rm_lines]
d <- gsub("##INFO=<ID=","",d)
sp2 <- strsplit(d, ",")
info_names <- unlist(lapply(sp2, `[[`, 1))
vcffile[,info_names] <- ""
# Funtzioa
vcffile$V8 <- as.character(vcffile$V8)
sp3 <- strsplit(vcffile$V8, ";")
locname <- function(x, info)
{
all_string <- x[grep(paste0("^",info,"="),x)]
value_only <- gsub(paste0(info,"="), "", all_string, )
value_only <- value_only[1]
# vcffile[h,info_names[g]] <- value_only[1]
if(length(value_only) == 0) value_only <- NA
return(value_only)
}
# Loop
for(g in 1:length(info_names))
{
print(paste0(g, "/", length(info_names)))
vcffile[,info_names[g]] <- unlist(lapply(sp3, locname, info = info_names[g]))
}
# un1 <- unlist(lapply(sp3, locname, info = info_names[g]))
# table(un1)
# Biltzen
dftot <- cbind(vcffile[,-c(8:10)],col10_fin)
names(dftot)[1:7] <- c("Chr","Pos","ID","Ref","Alt","QUAL","Filt")
numvar <- c("Pos","ID","DP","esp6500siv2_ea",
"SIFT_score","Polyphen2_HDIV_score","Polyphen2_HVAR_score","LRT_score",
"MutationTaster_score","MutationAssessor_score","FATHMM_score","PROVEAN_score",
"VEST3_score","CADD_raw","CADD_phred","DANN_score","fathmm-MKL_coding_score",
"MetaSVM_score","MetaLR_score","integrated_fitCons_score",
"integrated_confidence_value", "GERPpp_RS",
"phyloP7way_vertebrate","phyloP20way_mammalian","phastCons7way_vertebrate",
"phastCons20way_mammalian","SiPhy_29way_logOdds","ExAC_ALL","ExAC_AFR","ExAC_AMR",
"ExAC_EAS","ExAC_FIN","ExAC_NFE","ExAC_OTH","ExAC_SAS",
"DP","AD1","AD2","PL1",
"PL2","PL3")
for(q in numvar)
{
dftot[,q] <- as.numeric(as.character(dftot[,q]))
}
# for(q in c(8:23,31,seq(38,64,2),66:71,75,76,78:82))
# {
# dftot[,q] <- as.numeric(as.character(dftot[,q]))
# }
if(save)
{
save(dftot, file = paste0(rdatafile, ".RData"))
write.csv(dftot, file = paste0(rdatafile, ".csv"))
}
}
# Somaticas
from_vcf2excel_somatica <- function(name_vcffile = "exome_pass_v011.vcf",
rdatafile = "20201125_vcf_Ex77801_s10",save = TRUE)
{
# setwd("Exoma/EXOMA_EAA001_V300056632_L02/")
# dir()
# name_vcffile = "exome_pass_v011.vcf"
vcffile <- utils::read.table(name_vcffile)
vcffile$V9 <- as.character(vcffile$V9)
OBQRC <- grep("OBQRC",vcffile$V9)
PGT <- grep("PGT",vcffile$V9)
table(vcffile$V9)
vcffile$OBQRC <- ifelse(rownames(vcffile)%in%OBQRC,"OBQRC",NA)
vcffile$PGT <- ifelse(rownames(vcffile)%in%PGT,"PGT",NA)
vcffile$group <- 0
vcffile$group[vcffile$OBQRC == "OBQRC" & is.na(vcffile$PGT)] <- 1
vcffile$group[vcffile$OBQRC == "OBQRC" & vcffile$PGT == "PGT"] <- 2
vcffile$group[is.na(vcffile$OBQRC) & is.na(vcffile$PGT)] <- 3
vcffile$group[vcffile$PGT == "PGT" & is.na(vcffile$OBQRC)] <- 4
vcffile$ID <- 1:(nrow(vcffile))
table(vcffile$group)
name_group <- names(table(vcffile$group))
# Extract names
u1 <- unique(vcffile$V9[vcffile$OBQRC == "OBQRC" & vcffile$PGT == "PGT"])
# if(!is.na(u1))
# {
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10[vcffile$group==1])
# g1_11 <- as.character(vcffile$V11[vcffile$group==1])
id_1 <- vcffile$ID[vcffile$group==1]
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = 12,byrow = TRUE))
col10c <- cbind(col10b,rep(NA,nrow(col10b)),rep(NA,nrow(col10b)),rep(NA,nrow(col10b)))
names(col10c) <- names9
# GROUP 2
g2_10 <- as.character(vcffile$V10[vcffile$group==2])
id_2 <- vcffile$ID[vcffile$group==2]
col210 <- unlist(strsplit(g2_10,":"))
col210b <- data.frame(matrix(col210,ncol = 15,byrow = TRUE))
col210c <- col210b
names(col210c) <- names9
# GROUP 3
g3_10 <- as.character(vcffile$V10[vcffile$group==3])
id_3 <- vcffile$ID[vcffile$group==3]
col310 <- unlist(strsplit(g3_10,":"))
col310b <- data.frame(matrix(col310,ncol = 8,byrow = TRUE))
col310c <- cbind(col310b[,1:8],data.frame(matrix(NA, nrow = nrow(col310b),ncol = 7, byrow = TRUE)))
names(col310c) <- names9
# GROUP 4
g4_10 <- as.character(vcffile$V10[vcffile$group==4])
id_4 <- vcffile$ID[vcffile$group==4]
col410 <- unlist(strsplit(g4_10,":"))
col410b <- data.frame(matrix(col410,ncol = 11,byrow = TRUE))
col410c <- cbind(col410b[,1:8],data.frame(matrix(NA, nrow = nrow(col410b),ncol = 4, byrow = TRUE)),col410b[,9:11])
names(col410c) <- names9
id_t <- c(id_1,id_2,id_3,id_4)
dfcol <- rbind(col10c,col210c,col310c,col410c)
# dfcol3 <- rbind(col11c,col211c,col311c,col411c)
dfcol2 <- cbind(id_t,dfcol)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
# names(dfcol2)[13:23]<- paste0(names(dfcol2)[2:12],"_tum")
dfcol2$AD <- as.character(dfcol2$AD)
dfcol2$F1R2 <- as.character(dfcol2$F1R2)
dfcol2$F2R1 <- as.character(dfcol2$F2R1)
add <- strsplit(dfcol2$AD, ",")
nadd <- unlist(lapply(add, length))
ad1a <- as.numeric(unlist(lapply(add, `[[`, 1)))
ad1b <- as.numeric(unlist(lapply(add, `[[`, 2)))
ad <- data.frame(ad1a, ad1b, nadd)
names(ad) <- c("AD_ref","AD_alt", "AD_n")
F1R2d <- strsplit(dfcol2$F1R2, ",")
nF1R2 <- unlist(lapply(F1R2d, length))
F1R21a <- as.numeric(unlist(lapply(F1R2d, `[[`, 1)))
F1R21b <- as.numeric(unlist(lapply(F1R2d, `[[`, 2)))
F1R2 <- data.frame(F1R21a, F1R21b, nF1R2)
names(F1R2) <- c("F1R2_ref","F1R2_alt","F1R2_n")
F2R1d <- strsplit(dfcol2$F2R1, ",")
nF2R1 <- unlist(lapply(F2R1d, length))
F2R11a <- as.numeric(unlist(lapply(F2R1d, `[[`, 1)))
F2R11b <- as.numeric(unlist(lapply(F2R1d, `[[`, 2)))
F2R1 <- data.frame(F2R11a, F2R11b, nF2R1)
names(F2R1) <- c("F2R1_ref","F2R1_alt", "F2R1_n")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1,3)],ad,dfcol2[,c(4:6)],F1R2,dfcol2[ ,7],F2R1,dfcol2[,c(8:ncol(dfcol2))])
# Read header
d <- readLines(name_vcffile, n = 1000)
rm_lines <- grep("INFO=",d)
d <- d[rm_lines]
d <- gsub("##INFO=<ID=","",d)
sp2 <- strsplit(d, ",")
info_names <- unlist(lapply(sp2, `[[`, 1))
vcffile[,info_names] <- ""
# Funtzioa
vcffile$V8 <- as.character(vcffile$V8)
sp3 <- strsplit(vcffile$V8, ";")
locname <- function(x, info)
{
all_string <- x[grep(paste0("^",info,"="),x)]
value_only <- gsub(paste0(info,"="), "", all_string, )
value_only <- value_only[1]
# vcffile[h,info_names[g]] <- value_only[1]
if(length(value_only) == 0) value_only <- NA
return(value_only)
}
# Loop
for(g in 1:length(info_names))
{
print(paste0(g, "/", length(info_names)))
vcffile[,info_names[g]] <- unlist(lapply(sp3, locname, info = info_names[g]))
}
# un1 <- unlist(lapply(sp3, locname, info = info_names[g]))
# table(un1)
# Biltzen
dftot <- cbind(vcffile[,-c(8:10)],formatfin)
names(dftot)[1:7] <- c("Chr","Pos","ID","Ref","Alt","QUAL","Filt")
numvar <- c("Pos","group","ID","CONTQ","DP","ECNT","GERMQ","esp6500siv2_ea",
"SIFT_score","Polyphen2_HDIV_score","Polyphen2_HVAR_score","LRT_score",
"MutationTaster_score","MutationAssessor_score","FATHMM_score","PROVEAN_score",
"VEST3_score","CADD_raw","CADD_phred","DANN_score","fathmm-MKL_coding_score",
"MetaSVM_score","MetaLR_score","integrated_fitCons_score",
"integrated_confidence_value", "GERPpp_RS",
"phyloP7way_vertebrate","phyloP20way_mammalian","phastCons7way_vertebrate",
"phastCons20way_mammalian","SiPhy_29way_logOdds","ExAC_ALL","ExAC_AFR","ExAC_AMR",
"ExAC_EAS","ExAC_FIN","ExAC_NFE","ExAC_OTH","ExAC_SAS",
"AD_ref","AD_alt","AD_n","AF","DP","F1R2_ref","F1R2_alt","F1R2_n",
"F2R1_ref","F2R1_alt","F2R1_n",
"OBF","OBP","OBQ","OBQRC")
for(q in numvar)
{
dftot[,q] <- as.numeric(as.character(dftot[,q]))
}
if(save)
{
save(dftot, file = paste0(rdatafile, ".RData"))
write.csv(dftot, file = paste0(rdatafile, ".csv"))
}
}
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