R/from_vcf2df.R
In itamuria/immunoeasy: Make Immuno Therapies An Easier Process
Defines functions
varscan_2_excel
somaticsniper_2_excel
strelka_indels_2_excel
strelka_2_excel_snvs_fast
strelka_2_excel
mutect38_2df
Documented in
mutect38_2df
somaticsniper_2_excel
strelka_2_excel
strelka_2_excel_snvs_fast
strelka_indels_2_excel
varscan_2_excel
#' From vcf to excel by mutect38__2df
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' mutect38__2df (name_vcffile)
#' }
#'
mutect38_2df <- function(name_vcffile, excel = FALSE, excel_file = "20200306_Mutect.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
fox <- grep("FOXOG",vcffile$V9)
pgt <- grep("PGT",vcffile$V9)
table(vcffile$V9)
vcffile$fox <- ifelse(rownames(vcffile)%in%fox,"Fox",NA)
vcffile$pgt <- ifelse(rownames(vcffile)%in%pgt,"Pgt",NA)
vcffile$group <- 0
vcffile$group[vcffile$fox == "Fox" & is.na(vcffile$pgt)] <- 1
vcffile$group[vcffile$fox == "Fox" & vcffile$pgt == "Pgt"] <- 2
vcffile$group[is.na(vcffile$fox) & is.na(vcffile$pgt)] <- 3
vcffile$group[vcffile$pgt == "Pgt" & is.na(vcffile$fox)] <- 4
vcffile$ID <- 1:(nrow(vcffile))
table(vcffile$group)
name_group <- names(table(vcffile$group))
# Extract names
u1 <- unique(vcffile$V9[vcffile$fox == "Fox" & vcffile$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 = 9,byrow = TRUE))
col10c <- cbind(col10b[,1:6],rep(NA,nrow(col10b)),rep(NA,nrow(col10b)),col10b[,7:9])
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = 9,byrow = TRUE))
col11c <- cbind(col11b[,1:6],rep(NA,nrow(col11b)),rep(NA,nrow(col11b)),col11b[,7:9])
names(col11c) <- names9
# GROUP 2
g2_10 <- as.character(vcffile$V10[vcffile$group==2])
g2_11 <- as.character(vcffile$V11[vcffile$group==2])
id_2 <- vcffile$ID[vcffile$group==2]
col210 <- unlist(strsplit(g2_10,":"))
col210b <- data.frame(matrix(col210,ncol = 11,byrow = TRUE))
col210c <- col210b
names(col210c) <- names9
col211 <- unlist(strsplit(g2_11,":"))
col211b <- data.frame(matrix(col211,ncol = 11,byrow = TRUE))
col211c <- col211b
names(col211c) <- names9
# GROUP 3
g3_10 <- as.character(vcffile$V10[vcffile$group==3])
g3_11 <- as.character(vcffile$V11[vcffile$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[,1:5],rep(NA,nrow(col310b)),rep(NA,nrow(col310b)),rep(NA,nrow(col310b)),col310b[,6:8])
names(col310c) <- names9
col311 <- unlist(strsplit(g3_11,":"))
col311b <- data.frame(matrix(col311,ncol = 8,byrow = TRUE))
col311c <- cbind(col311b[,1:5],rep(NA,nrow(col311b)),rep(NA,nrow(col311b)),rep(NA,nrow(col311b)),col311b[,6:8])
names(col311c) <- names9
# GROUP 4
g4_10 <- as.character(vcffile$V10[vcffile$group==4])
g4_11 <- as.character(vcffile$V11[vcffile$group==4])
id_4 <- vcffile$ID[vcffile$group==4]
col410 <- unlist(strsplit(g4_10,":"))
col410b <- data.frame(matrix(col410,ncol = 10,byrow = TRUE))
col410c <- cbind(col410b[,1:5],rep(NA,nrow(col410b)),col410b[,6:10])
names(col410c) <- names9
col411 <- unlist(strsplit(g4_11,":"))
col411b <- data.frame(matrix(col411,ncol = 10,byrow = TRUE))
col411c <- cbind(col411b[,1:5],rep(NA,nrow(col411b)),col411b[,6:10])
names(col411c) <- 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,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
names(dfcol2)[13:23]<- paste0(names(dfcol2)[2:12],"_tum")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AD),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("AD_ref","AD_alt")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$QSS),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("QSS_ref","QSS_alt")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AD_tum),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("AD_ref_tum","AD_alt_tum")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$QSS_tum),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("QSS_ref_tum","QSS_alt_tum")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1,2)],ad1,dfcol2[,c(4:8)],gss1,dfcol2[,c(11,13)],ad1b,dfcol2[,c(15:20)],gss1b,dfcol2[,c(22,23)])
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:58), sep = ";")
s2 <- s1[,c(8:65)]
s2[grep("RPA",s2$a6),names(s2)] <- s2[grep("RPA",s2$a6),names(s2)[-c(6:8)]]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[seq(1,110,by = 2)]
for(h in c(1:41,43:58))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
names(s2)[42]<- "GERP"
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
for(q in c(2,68:73,75:77,79:84,87:90))
{
dftot[,q] <- as.numeric(as.character(dftot[,q]))
}
dftot$Cob_DNA_nor <- dftot$AD_ref+dftot$AD_alt
dftot$Cob_DNA_tum <- dftot$AD_ref_tum+dftot$AD_alt_tum
dftot <- dftot[,!is.na(names(dftot))]
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by Strelka
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
# cuidado con GT, no quitar o cambiar codigo despues de cambiar
strelka_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_strelka.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
# names9 <- names9[-1]
# names9 <- names9[-1]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
# nchar(g1_10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("AU_T1","AU_T2")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("CU_T1","CU_T2")
gss2 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU),",")),ncol = 2,byrow = TRUE))
names(gss2) <- c("GU_T1","GU_T2")
gss3 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU),",")),ncol = 2,byrow = TRUE))
names(gss3) <- c("TU_T1","TU_T2")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU_2),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("AU_T1_2","AU_T2_2")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU_2),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("CU_T1_2","CU_T2_2")
gss2b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU_2),",")),ncol = 2,byrow = TRUE))
names(gss2b) <- c("GU_T1_2","GU_T2_2")
gss3b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU),",")),ncol = 2,byrow = TRUE))
names(gss3b) <- c("TU_T1_2","TU_T2_2")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:5)],ad1,gss1,gss2,gss3,dfcol2[,c(10:13)],ad1b,gss1b,gss2b,gss3b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:60), sep = ";")
s2 <- s1[,c(8:67)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(1,seq(2,118,by = 2))]
for(h in c(2:48,50:60))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
# plot(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor.test(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
#
# plot(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor.test(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
for(y in 69:ncol(dftot))
{
dftot[,y] <- as.numeric(as.character(dftot[,y]))
}
dftot$Ref_T1 <- 0
dftot$Alt_T1 <- 0
dftot$Ref_T2 <- 0
dftot$Alt_T2 <- 0
for(q in 1:nrow(dftot))
{
print(paste0(q,"/",nrow(dftot)))
dftot$Ref_T1[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T1"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T1"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T1"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T1"],NA))))
dftot$Ref_T2[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T2"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T2"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T2"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T2"],NA))))
dftot$Alt_T1[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T1"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T1"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T1"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T1"],NA))))
dftot$Alt_T2[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T2"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T2"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T2"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T2"],NA))))
}
dftot$Ref_T1_2 <- 0
dftot$Alt_T1_2 <- 0
dftot$Ref_T2_2 <- 0
dftot$Alt_T2_2 <- 0
for(q in 1:nrow(dftot))
{
print(paste0(q,"/",nrow(dftot)))
dftot$Ref_T1_2[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T1_2"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T1_2"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T1_2"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T1_2"],NA))))
dftot$Ref_T2_2[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T2_2"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T2_2"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T2_2"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T2_2"],NA))))
dftot$Alt_T1_2[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T1_2"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T1_2"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T1_2"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T1_2"],NA))))
dftot$Alt_T2_2[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T2_2"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T2_2"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T2_2"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T2_2"],NA))))
}
dftote <- dftot
dftot[dftot$NT=="hom",c("Ref_T1","Ref_T2","Ref_T1_2","Ref_T2_2")] <- dftote[dftote$NT=="hom",c("Alt_T1","Alt_T2","Alt_T1_2","Alt_T2_2")]
dftot[dftot$NT=="hom",c("Alt_T1","Alt_T2","Alt_T1_2","Alt_T2_2")] <- dftote[dftote$NT=="hom",c("Ref_T1","Ref_T2","Ref_T1_2","Ref_T2_2")]
dftot$VAF_T1 <- dftot$Alt_T1_2/(dftot$Alt_T1_2+dftot$Ref_T1_2)
dftot$VAF_T2 <- dftot$Alt_T2_2/(dftot$Alt_T2_2+dftot$Ref_T2_2)
# ff <- dftot$Ref_T1-dftot$Alt_T1
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
# aggregate(ff,by=list(dftot$NT),FUN=function(x) c(min(x),mean(x),max(x)))
return(dftot)
}
#' From vcf to excel by Strelka fast version
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
strelka_2_excel_snvs_fast <- function(name_vcffile, excel = FALSE, excel_file = "20200306_strelka_snvs.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
# names9 <- names9[-1]
# names9 <- names9[-1]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
nchar(g1_10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("AU_T1_normal","AU_T2_normal")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("CU_T1_normal","CU_T2_normal")
gss2 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU),",")),ncol = 2,byrow = TRUE))
names(gss2) <- c("GU_T1_normal","GU_T2_normal")
gss3 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU),",")),ncol = 2,byrow = TRUE))
names(gss3) <- c("TU_T1_normal","TU_T2_normal")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU_2),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("AU_T1_tumor","AU_T2_tumor")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU_2),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("CU_T1_tumor","CU_T2_tumor")
gss2b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU_2),",")),ncol = 2,byrow = TRUE))
names(gss2b) <- c("GU_T1_tumor","GU_T2_tumor")
gss3b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU_2),",")),ncol = 2,byrow = TRUE))
names(gss3b) <- c("TU_T1_tumor","TU_T2_tumor")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:5)],ad1,gss1,gss2,gss3,dfcol2[,c(10:13)],ad1b,gss1b,gss2b,gss3b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:60), sep = ";")
s2 <- s1[,c(8:67)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(1,seq(2,118,by = 2))]
for(h in c(2:48,50:60))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
# plot(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor.test(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
#
# plot(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor.test(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
for(y in 29:ncol(dftot))
{
dftot[,y] <- as.numeric(as.character(dftot[,y]))
}
dftot$Ref_T1_normal <- 0
dftot$Alt_T1_normal <- 0
dftot$Ref_T2_normal <- 0
dftot$Alt_T2_normal <- 0
dftot$Ref_T1_normal <- ifelse(dftot$Ref=="A",dftot[,"AU_T1_normal"],
ifelse(dftot$Ref=="C",dftot[,"CU_T1_normal"],
ifelse(dftot$Ref=="G",dftot[,"GU_T1_normal"],
ifelse(dftot$Ref=="T",dftot[,"TU_T1_normal"],NA))))
dftot$Ref_T2_normal <- ifelse(dftot$Ref=="A",dftot[,"AU_T2_normal"],
ifelse(dftot$Ref=="C",dftot[,"CU_T2_normal"],
ifelse(dftot$Ref=="G",dftot[,"GU_T2_normal"],
ifelse(dftot$Ref=="T",dftot[,"TU_T2_normal"],NA))))
dftot$Alt_T1_normal <- ifelse(dftot$Alt=="A",dftot[,"AU_T1_normal"],
ifelse(dftot$Alt=="C",dftot[,"CU_T1_normal"],
ifelse(dftot$Alt=="G",dftot[,"GU_T1_normal"],
ifelse(dftot$Alt=="T",dftot[,"TU_T1_normal"],NA))))
dftot$Alt_T2_normal <- ifelse(dftot$Alt=="A",dftot[,"AU_T2_normal"],
ifelse(dftot$Alt=="C",dftot[,"CU_T2_normal"],
ifelse(dftot$Alt=="G",dftot[,"GU_T2_normal"],
ifelse(dftot$Alt=="T",dftot[,"TU_T2_normal"],NA))))
dftot$Ref_T1_tumor <- 0
dftot$Alt_T1_tumor <- 0
dftot$Ref_T2_tumor <- 0
dftot$Alt_T2_tumor <- 0
dftot$Ref_T1_tumor <- ifelse(dftot$Ref=="A",dftot[,"AU_T1_tumor"],
ifelse(dftot$Ref=="C",dftot[,"CU_T1_tumor"],
ifelse(dftot$Ref=="G",dftot[,"GU_T1_tumor"],
ifelse(dftot$Ref=="T",dftot[,"TU_T1_tumor"],NA))))
dftot$Ref_T2_tumor <- ifelse(dftot$Ref=="A",dftot[,"AU_T2_tumor"],
ifelse(dftot$Ref=="C",dftot[,"CU_T2_tumor"],
ifelse(dftot$Ref=="G",dftot[,"GU_T2_tumor"],
ifelse(dftot$Ref=="T",dftot[,"TU_T2_tumor"],NA))))
dftot$Alt_T1_tumor <- ifelse(dftot$Alt=="A",dftot[,"AU_T1_tumor"],
ifelse(dftot$Alt=="C",dftot[,"CU_T1_tumor"],
ifelse(dftot$Alt=="G",dftot[,"GU_T1_tumor"],
ifelse(dftot$Alt=="T",dftot[,"TU_T1_tumor"],NA))))
dftot$Alt_T2_tumor <- ifelse(dftot$Alt=="A",dftot[,"AU_T2_tumor"],
ifelse(dftot$Alt=="C",dftot[,"CU_T2_tumor"],
ifelse(dftot$Alt=="G",dftot[,"GU_T2_tumor"],
ifelse(dftot$Alt=="T",dftot[,"TU_T2_tumor"],NA))))
dftote <- dftot
dftot[dftot$NT=="hom",c("Ref_T1_normal","Ref_T2_normal","Ref_T1_tumor","Ref_T2_tumor")] <- dftote[dftote$NT=="hom",c("Alt_T1_normal","Alt_T2_normal","Alt_T1_tumor","Alt_T2_tumor")]
dftot[dftot$NT=="hom",c("Alt_T1_normal","Alt_T2_normal","Alt_T1_tumor","Alt_T2_tumor")] <- dftote[dftote$NT=="hom",c("Ref_T1_normal","Ref_T2_normal","Ref_T1_tumor","Ref_T2_tumor")]
dftot$VAF_T1 <- dftot$Alt_T1_tumor/(dftot$Alt_T1_tumor+dftot$Ref_T1_tumor)
dftot$VAF_T2 <- dftot$Alt_T2_tumor/(dftot$Alt_T2_tumor+dftot$Ref_T2_tumor)
# ff <- dftot$Ref_T1-dftot$Alt_T1
# aggregate(ff,by=list(dftot$NT),FUN=function(x) c(min(x),mean(x),max(x)))
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by Strelka for indels
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
strelka_indels_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_strelka_indels.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
# names9 <- names9[-1]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TAR),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("TAR_T1","TAR_T2")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TIR),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("TIR_T1","TIR_T2")
gss2 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TOR),",")),ncol = 2,byrow = TRUE))
names(gss2) <- c("TOR_T1","TOR_T2")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TAR_2),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("TAR_T1_2","TAR_T2_2")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TIR_2),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("TIR_T1_2","TIR_T2_2")
gss2b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TOR_2),",")),ncol = 2,byrow = TRUE))
names(gss2b) <- c("TOR_T1_2","TOR_T2_2")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:3)],ad1,gss1,gss2,dfcol2[,c(7:12)],ad1b,gss1b,gss2b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:60), sep = ";")
s2 <- s1[,c(8:67)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(1,seq(2,118,by = 2))]
for(h in c(2:49,51:60))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
dftot$TIR_T1_2 <- as.numeric(as.character(dftot$TIR_T1_2))
dftot$TAR_T1_2 <- as.numeric(as.character(dftot$TAR_T1_2))
dftot$vaf <- dftot$TIR_T1_2/(dftot$TIR_T1_2+dftot$TAR_T1_2)
naw <- which(is.na(names(dftot)))
if(length(naw)>0)
{
dftot <- dftot[,-naw]
}
pos1 <- which(names(dftot)=="DP")
for(g in pos1:ncol(dftot))
{
dftot[,g] <- as.numeric(as.character(dftot[,g]))
}
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by somatic sniper
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
somaticsniper_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_somaticsniper.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$DP4),",")),ncol = 4,byrow = TRUE))
names(ad1) <- c("Norm_DP_ref_forw","Norm_DP_ref_rev","Norm_DP_alt_forw","Norm_DP_alt_rev")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT),",")),ncol = 4,byrow = TRUE))
names(gss1) <- c("NormCOUNT_A","NormCOUNT_C","NormCOUNT_G","NormCOUNT_T")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$DP4_2),",")),ncol = 4,byrow = TRUE))
names(ad1b) <- c("Tum_DP_ref_forw","Tum_DP_ref_rev","Tum_DP_alt_forw","Tum_DP_alt_rev")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT_2),",")),ncol = 4,byrow = TRUE))
names(gss1b) <- c("TumCOUNT_A","TumCOUNT_C","TumCOUNT_G","TumCOUNT_T")
for(t in 1:4)
{
ad1[,t] <- as.numeric(as.character(ad1[,t]))
ad1b[,t] <- as.numeric(as.character(ad1b[,t]))
}
alt1 <- ad1$Norm_DP_alt_forw+ad1$Norm_DP_alt_rev
alt2 <- ad1b$Tum_DP_alt_forw+ad1b$Tum_DP_alt_rev
dfcol2$DP <- as.numeric(as.character(dfcol2$DP))
dfcol2$DP_2 <- as.numeric(as.character(dfcol2$DP_2))
vaf1 <- alt1/dfcol2$DP
vaf2 <- alt2/dfcol2$DP_2
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:4)],ad1,alt1,vaf1,gss1,dfcol2[,c(7:17)],ad1b,alt2,vaf2,gss1b,dfcol2[,c(20:27)])
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:48), sep = ";")
s2 <- s1[,c(8:58)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(seq(2,94,by = 2))]
for(h in c(1:35,37:47))
{
print(h)
s2[,h+1] <- gsub(paste0(snames2[h],"="),"",s2[,h+1])
names(s2)[h+1] <- snames2[h]
}
names(s2)[37] <- "GERP"
# s2[,37] <- gsub(paste0("GERP++_RS=.","",s2[,h+1]))
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
nakendu <- sapply(dftot, function(e) {
len1 <- length(e)
pr90 <- len1 * 90 / 100
pr90 < sum(is.na(e))
})
dftot <- dftot[,!nakendu]
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by varscan
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
varscan_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_varscan.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0("Tum_",names(dfcol2)[2:(nnc2+1)])
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$DP4),",")),ncol = 4,byrow = TRUE))
names(ad1) <- c("Nor_Ref_ST_p","Nor_Ref_ST_n","Nor_Alt_ST_p","Nor_Alt_ST_n")
# gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT),",")),ncol = 4,byrow = TRUE))
# names(gss1) <- c("BCOUNT_ref","BCOUNT_alt","BCOUNT_3","BCOUNT_4")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$Tum_DP4),",")),ncol = 4,byrow = TRUE))
names(ad1b) <- c("Tum_Ref_ST_p","Tum_Ref_ST_n","Tum_Alt_ST_p","Tum_Alt_ST_n")
# gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT_2),",")),ncol = 4,byrow = TRUE))
# names(gss1b) <- c("BCOUNT_ref_2","BCOUNT_alt_2","BCOUNT_2_3","BCOUNT_2_4")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:7)],ad1,dfcol2[,c(9:14)],ad1b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:53), sep = ";")
s2 <- s1[,c(8,10:60)]
# s2 <- s2[,-2]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(seq(1,106,by = 2))]
azkeNA <- which(is.na(snames2))[1]-1
for(h in c(1:azkeNA))
{
print(h)
if(length(grep("GERP\\+\\+_RS", snames2[h]))>0)
{
s2[,h] <- gsub("GERP\\+\\+_RS","GERP_RS",s2[,h])
snames2[h] <- gsub("GERP\\+\\+_RS","GERP_RS",snames2[h])
}
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
kendu <- sapply(s2,function(x)
{
nr <- length(x)
sr <- sum(is.na(x))
nr!=sr
})
tt <- table(kendu)
if(length(tt)>1) s2 <- s2[,kendu]
names(s2)[which(names(s2)=="DP")] <- "DP_Tum_Nor"
# names(s2)[42] <- "GERP"
# s2[,37] <- gsub(paste0("GERP++_RS=.","",s2[,h+1]))
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
names(dftot)[which(names(dftot)=="RD")] <- "Nor_Ref_D"
names(dftot)[which(names(dftot)=="DP")] <- "Nor_DP"
names(dftot)[which(names(dftot)=="AD")] <- "Nor_Alt_D"
names(dftot)[which(names(dftot)=="Tum_RD")] <- "Tum_Ref_D"
names(dftot)[which(names(dftot)=="Tum_AD")] <- "Tum_Alt_D"
w_names <- which(names(dftot)%in%c("Pos","DP_Tum_Nor","SSC","GPV","SPV","id_t","Nor_DP","Nor_Ref_D","Nor_Alt_D","Nor_Ref_ST_p" ,"Nor_Ref_ST_n", "Nor_Alt_ST_p", "Nor_Alt_ST_n",
"Tum_DP","Tum_Ref_D","Tum_Alt_D","Tum_Ref_ST_p","Tum_Ref_ST_n","Tum_Alt_ST_p","Tum_Alt_ST_n"))
for(z in w_names)
{
dftot[,z] <- as.numeric(as.character(dftot[,z]))
}
dftot$Tum_Ratio_Alt_st <- dftot$Tum_Alt_ST_p/dftot$Tum_Alt_ST_n
dftot$FREQ <- as.character(dftot$FREQ)
dftot$FREQ <- as.numeric(gsub("%","",dftot$FREQ))
dftot$Tum_FREQ <- as.character(dftot$Tum_FREQ)
dftot$Tum_FREQ <- as.numeric(gsub("%","",dftot$Tum_FREQ))
dftot$Tum_FREQ <- dftot$Tum_FREQ/100
dftot$FREQ <- dftot$FREQ/100
names(dftot)[which(names(dftot)=="FREQ")] <- "Nor_VAF"
names(dftot)[which(names(dftot)=="Tum_FREQ")] <- "Tum_VAF"
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
itamuria/immunoeasy documentation built on Sept. 30, 2022, 5:53 a.m.
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Defines functions varscan_2_excel somaticsniper_2_excel strelka_indels_2_excel strelka_2_excel_snvs_fast strelka_2_excel mutect38_2df
Documented in mutect38_2df somaticsniper_2_excel strelka_2_excel strelka_2_excel_snvs_fast strelka_indels_2_excel varscan_2_excel
#' From vcf to excel by mutect38__2df
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' mutect38__2df (name_vcffile)
#' }
#'
mutect38_2df <- function(name_vcffile, excel = FALSE, excel_file = "20200306_Mutect.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
fox <- grep("FOXOG",vcffile$V9)
pgt <- grep("PGT",vcffile$V9)
table(vcffile$V9)
vcffile$fox <- ifelse(rownames(vcffile)%in%fox,"Fox",NA)
vcffile$pgt <- ifelse(rownames(vcffile)%in%pgt,"Pgt",NA)
vcffile$group <- 0
vcffile$group[vcffile$fox == "Fox" & is.na(vcffile$pgt)] <- 1
vcffile$group[vcffile$fox == "Fox" & vcffile$pgt == "Pgt"] <- 2
vcffile$group[is.na(vcffile$fox) & is.na(vcffile$pgt)] <- 3
vcffile$group[vcffile$pgt == "Pgt" & is.na(vcffile$fox)] <- 4
vcffile$ID <- 1:(nrow(vcffile))
table(vcffile$group)
name_group <- names(table(vcffile$group))
# Extract names
u1 <- unique(vcffile$V9[vcffile$fox == "Fox" & vcffile$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 = 9,byrow = TRUE))
col10c <- cbind(col10b[,1:6],rep(NA,nrow(col10b)),rep(NA,nrow(col10b)),col10b[,7:9])
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = 9,byrow = TRUE))
col11c <- cbind(col11b[,1:6],rep(NA,nrow(col11b)),rep(NA,nrow(col11b)),col11b[,7:9])
names(col11c) <- names9
# GROUP 2
g2_10 <- as.character(vcffile$V10[vcffile$group==2])
g2_11 <- as.character(vcffile$V11[vcffile$group==2])
id_2 <- vcffile$ID[vcffile$group==2]
col210 <- unlist(strsplit(g2_10,":"))
col210b <- data.frame(matrix(col210,ncol = 11,byrow = TRUE))
col210c <- col210b
names(col210c) <- names9
col211 <- unlist(strsplit(g2_11,":"))
col211b <- data.frame(matrix(col211,ncol = 11,byrow = TRUE))
col211c <- col211b
names(col211c) <- names9
# GROUP 3
g3_10 <- as.character(vcffile$V10[vcffile$group==3])
g3_11 <- as.character(vcffile$V11[vcffile$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[,1:5],rep(NA,nrow(col310b)),rep(NA,nrow(col310b)),rep(NA,nrow(col310b)),col310b[,6:8])
names(col310c) <- names9
col311 <- unlist(strsplit(g3_11,":"))
col311b <- data.frame(matrix(col311,ncol = 8,byrow = TRUE))
col311c <- cbind(col311b[,1:5],rep(NA,nrow(col311b)),rep(NA,nrow(col311b)),rep(NA,nrow(col311b)),col311b[,6:8])
names(col311c) <- names9
# GROUP 4
g4_10 <- as.character(vcffile$V10[vcffile$group==4])
g4_11 <- as.character(vcffile$V11[vcffile$group==4])
id_4 <- vcffile$ID[vcffile$group==4]
col410 <- unlist(strsplit(g4_10,":"))
col410b <- data.frame(matrix(col410,ncol = 10,byrow = TRUE))
col410c <- cbind(col410b[,1:5],rep(NA,nrow(col410b)),col410b[,6:10])
names(col410c) <- names9
col411 <- unlist(strsplit(g4_11,":"))
col411b <- data.frame(matrix(col411,ncol = 10,byrow = TRUE))
col411c <- cbind(col411b[,1:5],rep(NA,nrow(col411b)),col411b[,6:10])
names(col411c) <- 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,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
names(dfcol2)[13:23]<- paste0(names(dfcol2)[2:12],"_tum")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AD),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("AD_ref","AD_alt")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$QSS),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("QSS_ref","QSS_alt")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AD_tum),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("AD_ref_tum","AD_alt_tum")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$QSS_tum),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("QSS_ref_tum","QSS_alt_tum")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1,2)],ad1,dfcol2[,c(4:8)],gss1,dfcol2[,c(11,13)],ad1b,dfcol2[,c(15:20)],gss1b,dfcol2[,c(22,23)])
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:58), sep = ";")
s2 <- s1[,c(8:65)]
s2[grep("RPA",s2$a6),names(s2)] <- s2[grep("RPA",s2$a6),names(s2)[-c(6:8)]]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[seq(1,110,by = 2)]
for(h in c(1:41,43:58))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
names(s2)[42]<- "GERP"
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
for(q in c(2,68:73,75:77,79:84,87:90))
{
dftot[,q] <- as.numeric(as.character(dftot[,q]))
}
dftot$Cob_DNA_nor <- dftot$AD_ref+dftot$AD_alt
dftot$Cob_DNA_tum <- dftot$AD_ref_tum+dftot$AD_alt_tum
dftot <- dftot[,!is.na(names(dftot))]
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by Strelka
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
# cuidado con GT, no quitar o cambiar codigo despues de cambiar
strelka_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_strelka.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
# names9 <- names9[-1]
# names9 <- names9[-1]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
# nchar(g1_10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("AU_T1","AU_T2")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("CU_T1","CU_T2")
gss2 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU),",")),ncol = 2,byrow = TRUE))
names(gss2) <- c("GU_T1","GU_T2")
gss3 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU),",")),ncol = 2,byrow = TRUE))
names(gss3) <- c("TU_T1","TU_T2")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU_2),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("AU_T1_2","AU_T2_2")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU_2),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("CU_T1_2","CU_T2_2")
gss2b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU_2),",")),ncol = 2,byrow = TRUE))
names(gss2b) <- c("GU_T1_2","GU_T2_2")
gss3b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU),",")),ncol = 2,byrow = TRUE))
names(gss3b) <- c("TU_T1_2","TU_T2_2")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:5)],ad1,gss1,gss2,gss3,dfcol2[,c(10:13)],ad1b,gss1b,gss2b,gss3b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:60), sep = ";")
s2 <- s1[,c(8:67)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(1,seq(2,118,by = 2))]
for(h in c(2:48,50:60))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
# plot(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor.test(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
#
# plot(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor.test(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
for(y in 69:ncol(dftot))
{
dftot[,y] <- as.numeric(as.character(dftot[,y]))
}
dftot$Ref_T1 <- 0
dftot$Alt_T1 <- 0
dftot$Ref_T2 <- 0
dftot$Alt_T2 <- 0
for(q in 1:nrow(dftot))
{
print(paste0(q,"/",nrow(dftot)))
dftot$Ref_T1[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T1"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T1"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T1"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T1"],NA))))
dftot$Ref_T2[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T2"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T2"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T2"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T2"],NA))))
dftot$Alt_T1[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T1"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T1"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T1"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T1"],NA))))
dftot$Alt_T2[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T2"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T2"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T2"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T2"],NA))))
}
dftot$Ref_T1_2 <- 0
dftot$Alt_T1_2 <- 0
dftot$Ref_T2_2 <- 0
dftot$Alt_T2_2 <- 0
for(q in 1:nrow(dftot))
{
print(paste0(q,"/",nrow(dftot)))
dftot$Ref_T1_2[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T1_2"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T1_2"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T1_2"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T1_2"],NA))))
dftot$Ref_T2_2[q] <- ifelse(dftot$Ref[q]=="A",dftot[q,"AU_T2_2"],
ifelse(dftot$Ref[q]=="C",dftot[q,"CU_T2_2"],
ifelse(dftot$Ref[q]=="G",dftot[q,"GU_T2_2"],
ifelse(dftot$Ref[q]=="T",dftot[q,"TU_T2_2"],NA))))
dftot$Alt_T1_2[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T1_2"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T1_2"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T1_2"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T1_2"],NA))))
dftot$Alt_T2_2[q] <- ifelse(dftot$Alt[q]=="A",dftot[q,"AU_T2_2"],
ifelse(dftot$Alt[q]=="C",dftot[q,"CU_T2_2"],
ifelse(dftot$Alt[q]=="G",dftot[q,"GU_T2_2"],
ifelse(dftot$Alt[q]=="T",dftot[q,"TU_T2_2"],NA))))
}
dftote <- dftot
dftot[dftot$NT=="hom",c("Ref_T1","Ref_T2","Ref_T1_2","Ref_T2_2")] <- dftote[dftote$NT=="hom",c("Alt_T1","Alt_T2","Alt_T1_2","Alt_T2_2")]
dftot[dftot$NT=="hom",c("Alt_T1","Alt_T2","Alt_T1_2","Alt_T2_2")] <- dftote[dftote$NT=="hom",c("Ref_T1","Ref_T2","Ref_T1_2","Ref_T2_2")]
dftot$VAF_T1 <- dftot$Alt_T1_2/(dftot$Alt_T1_2+dftot$Ref_T1_2)
dftot$VAF_T2 <- dftot$Alt_T2_2/(dftot$Alt_T2_2+dftot$Ref_T2_2)
# ff <- dftot$Ref_T1-dftot$Alt_T1
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
# aggregate(ff,by=list(dftot$NT),FUN=function(x) c(min(x),mean(x),max(x)))
return(dftot)
}
#' From vcf to excel by Strelka fast version
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
strelka_2_excel_snvs_fast <- function(name_vcffile, excel = FALSE, excel_file = "20200306_strelka_snvs.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
# names9 <- names9[-1]
# names9 <- names9[-1]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
nchar(g1_10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("AU_T1_normal","AU_T2_normal")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("CU_T1_normal","CU_T2_normal")
gss2 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU),",")),ncol = 2,byrow = TRUE))
names(gss2) <- c("GU_T1_normal","GU_T2_normal")
gss3 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU),",")),ncol = 2,byrow = TRUE))
names(gss3) <- c("TU_T1_normal","TU_T2_normal")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$AU_2),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("AU_T1_tumor","AU_T2_tumor")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$CU_2),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("CU_T1_tumor","CU_T2_tumor")
gss2b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$GU_2),",")),ncol = 2,byrow = TRUE))
names(gss2b) <- c("GU_T1_tumor","GU_T2_tumor")
gss3b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TU_2),",")),ncol = 2,byrow = TRUE))
names(gss3b) <- c("TU_T1_tumor","TU_T2_tumor")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:5)],ad1,gss1,gss2,gss3,dfcol2[,c(10:13)],ad1b,gss1b,gss2b,gss3b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:60), sep = ";")
s2 <- s1[,c(8:67)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(1,seq(2,118,by = 2))]
for(h in c(2:48,50:60))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
# plot(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
# cor.test(as.numeric(dftot$AU_T1),as.numeric(dftot$AU_T2))
#
# plot(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
# cor.test(as.numeric(dftot$GU_T1),as.numeric(dftot$GU_T2))
for(y in 29:ncol(dftot))
{
dftot[,y] <- as.numeric(as.character(dftot[,y]))
}
dftot$Ref_T1_normal <- 0
dftot$Alt_T1_normal <- 0
dftot$Ref_T2_normal <- 0
dftot$Alt_T2_normal <- 0
dftot$Ref_T1_normal <- ifelse(dftot$Ref=="A",dftot[,"AU_T1_normal"],
ifelse(dftot$Ref=="C",dftot[,"CU_T1_normal"],
ifelse(dftot$Ref=="G",dftot[,"GU_T1_normal"],
ifelse(dftot$Ref=="T",dftot[,"TU_T1_normal"],NA))))
dftot$Ref_T2_normal <- ifelse(dftot$Ref=="A",dftot[,"AU_T2_normal"],
ifelse(dftot$Ref=="C",dftot[,"CU_T2_normal"],
ifelse(dftot$Ref=="G",dftot[,"GU_T2_normal"],
ifelse(dftot$Ref=="T",dftot[,"TU_T2_normal"],NA))))
dftot$Alt_T1_normal <- ifelse(dftot$Alt=="A",dftot[,"AU_T1_normal"],
ifelse(dftot$Alt=="C",dftot[,"CU_T1_normal"],
ifelse(dftot$Alt=="G",dftot[,"GU_T1_normal"],
ifelse(dftot$Alt=="T",dftot[,"TU_T1_normal"],NA))))
dftot$Alt_T2_normal <- ifelse(dftot$Alt=="A",dftot[,"AU_T2_normal"],
ifelse(dftot$Alt=="C",dftot[,"CU_T2_normal"],
ifelse(dftot$Alt=="G",dftot[,"GU_T2_normal"],
ifelse(dftot$Alt=="T",dftot[,"TU_T2_normal"],NA))))
dftot$Ref_T1_tumor <- 0
dftot$Alt_T1_tumor <- 0
dftot$Ref_T2_tumor <- 0
dftot$Alt_T2_tumor <- 0
dftot$Ref_T1_tumor <- ifelse(dftot$Ref=="A",dftot[,"AU_T1_tumor"],
ifelse(dftot$Ref=="C",dftot[,"CU_T1_tumor"],
ifelse(dftot$Ref=="G",dftot[,"GU_T1_tumor"],
ifelse(dftot$Ref=="T",dftot[,"TU_T1_tumor"],NA))))
dftot$Ref_T2_tumor <- ifelse(dftot$Ref=="A",dftot[,"AU_T2_tumor"],
ifelse(dftot$Ref=="C",dftot[,"CU_T2_tumor"],
ifelse(dftot$Ref=="G",dftot[,"GU_T2_tumor"],
ifelse(dftot$Ref=="T",dftot[,"TU_T2_tumor"],NA))))
dftot$Alt_T1_tumor <- ifelse(dftot$Alt=="A",dftot[,"AU_T1_tumor"],
ifelse(dftot$Alt=="C",dftot[,"CU_T1_tumor"],
ifelse(dftot$Alt=="G",dftot[,"GU_T1_tumor"],
ifelse(dftot$Alt=="T",dftot[,"TU_T1_tumor"],NA))))
dftot$Alt_T2_tumor <- ifelse(dftot$Alt=="A",dftot[,"AU_T2_tumor"],
ifelse(dftot$Alt=="C",dftot[,"CU_T2_tumor"],
ifelse(dftot$Alt=="G",dftot[,"GU_T2_tumor"],
ifelse(dftot$Alt=="T",dftot[,"TU_T2_tumor"],NA))))
dftote <- dftot
dftot[dftot$NT=="hom",c("Ref_T1_normal","Ref_T2_normal","Ref_T1_tumor","Ref_T2_tumor")] <- dftote[dftote$NT=="hom",c("Alt_T1_normal","Alt_T2_normal","Alt_T1_tumor","Alt_T2_tumor")]
dftot[dftot$NT=="hom",c("Alt_T1_normal","Alt_T2_normal","Alt_T1_tumor","Alt_T2_tumor")] <- dftote[dftote$NT=="hom",c("Ref_T1_normal","Ref_T2_normal","Ref_T1_tumor","Ref_T2_tumor")]
dftot$VAF_T1 <- dftot$Alt_T1_tumor/(dftot$Alt_T1_tumor+dftot$Ref_T1_tumor)
dftot$VAF_T2 <- dftot$Alt_T2_tumor/(dftot$Alt_T2_tumor+dftot$Ref_T2_tumor)
# ff <- dftot$Ref_T1-dftot$Alt_T1
# aggregate(ff,by=list(dftot$NT),FUN=function(x) c(min(x),mean(x),max(x)))
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by Strelka for indels
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
strelka_indels_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_strelka_indels.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
# names9 <- names9[-1]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TAR),",")),ncol = 2,byrow = TRUE))
names(ad1) <- c("TAR_T1","TAR_T2")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TIR),",")),ncol = 2,byrow = TRUE))
names(gss1) <- c("TIR_T1","TIR_T2")
gss2 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TOR),",")),ncol = 2,byrow = TRUE))
names(gss2) <- c("TOR_T1","TOR_T2")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TAR_2),",")),ncol = 2,byrow = TRUE))
names(ad1b) <- c("TAR_T1_2","TAR_T2_2")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TIR_2),",")),ncol = 2,byrow = TRUE))
names(gss1b) <- c("TIR_T1_2","TIR_T2_2")
gss2b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$TOR_2),",")),ncol = 2,byrow = TRUE))
names(gss2b) <- c("TOR_T1_2","TOR_T2_2")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:3)],ad1,gss1,gss2,dfcol2[,c(7:12)],ad1b,gss1b,gss2b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:60), sep = ";")
s2 <- s1[,c(8:67)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(1,seq(2,118,by = 2))]
for(h in c(2:49,51:60))
{
print(h)
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
dftot$TIR_T1_2 <- as.numeric(as.character(dftot$TIR_T1_2))
dftot$TAR_T1_2 <- as.numeric(as.character(dftot$TAR_T1_2))
dftot$vaf <- dftot$TIR_T1_2/(dftot$TIR_T1_2+dftot$TAR_T1_2)
naw <- which(is.na(names(dftot)))
if(length(naw)>0)
{
dftot <- dftot[,-naw]
}
pos1 <- which(names(dftot)=="DP")
for(g in pos1:ncol(dftot))
{
dftot[,g] <- as.numeric(as.character(dftot[,g]))
}
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by somatic sniper
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
somaticsniper_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_somaticsniper.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0(names(dfcol2)[2:(nnc2+1)],"_2")
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$DP4),",")),ncol = 4,byrow = TRUE))
names(ad1) <- c("Norm_DP_ref_forw","Norm_DP_ref_rev","Norm_DP_alt_forw","Norm_DP_alt_rev")
gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT),",")),ncol = 4,byrow = TRUE))
names(gss1) <- c("NormCOUNT_A","NormCOUNT_C","NormCOUNT_G","NormCOUNT_T")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$DP4_2),",")),ncol = 4,byrow = TRUE))
names(ad1b) <- c("Tum_DP_ref_forw","Tum_DP_ref_rev","Tum_DP_alt_forw","Tum_DP_alt_rev")
gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT_2),",")),ncol = 4,byrow = TRUE))
names(gss1b) <- c("TumCOUNT_A","TumCOUNT_C","TumCOUNT_G","TumCOUNT_T")
for(t in 1:4)
{
ad1[,t] <- as.numeric(as.character(ad1[,t]))
ad1b[,t] <- as.numeric(as.character(ad1b[,t]))
}
alt1 <- ad1$Norm_DP_alt_forw+ad1$Norm_DP_alt_rev
alt2 <- ad1b$Tum_DP_alt_forw+ad1b$Tum_DP_alt_rev
dfcol2$DP <- as.numeric(as.character(dfcol2$DP))
dfcol2$DP_2 <- as.numeric(as.character(dfcol2$DP_2))
vaf1 <- alt1/dfcol2$DP
vaf2 <- alt2/dfcol2$DP_2
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:4)],ad1,alt1,vaf1,gss1,dfcol2[,c(7:17)],ad1b,alt2,vaf2,gss1b,dfcol2[,c(20:27)])
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:48), sep = ";")
s2 <- s1[,c(8:58)]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(seq(2,94,by = 2))]
for(h in c(1:35,37:47))
{
print(h)
s2[,h+1] <- gsub(paste0(snames2[h],"="),"",s2[,h+1])
names(s2)[h+1] <- snames2[h]
}
names(s2)[37] <- "GERP"
# s2[,37] <- gsub(paste0("GERP++_RS=.","",s2[,h+1]))
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
nakendu <- sapply(dftot, function(e) {
len1 <- length(e)
pr90 <- len1 * 90 / 100
pr90 < sum(is.na(e))
})
dftot <- dftot[,!nakendu]
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
#' From vcf to excel by varscan
#'
#' @param name_vcffile The name of the vcf file
#' @param excel If we want to export to excel (boolean)
#' @param excel_file Name of the output excel file.
#'
#' @return data frame with ordered information
#' @export
#'
#' @examples
#' \dontrun{
#' strelka_2_excel (name_vcffile)
#' }
#'
varscan_2_excel <- function(name_vcffile, excel = FALSE, excel_file = "20200306_varscan.xlsx")
{
vcffile <- utils::read.table(name_vcffile)
# separate format
vcffile$V9 <- as.character(vcffile$V9)
vcffile$ID <- 1:(nrow(vcffile))
# Extract names
u1 <- unique(vcffile$V9)
u1 <- u1[!is.na(u1)]
names9 <- strsplit(u1,":")[[1]]
len9 <- length(names9)
# GROUP 1
g1_10 <- as.character(vcffile$V10)
g1_11 <- as.character(vcffile$V11)
id_1 <- vcffile$ID
col10 <- unlist(strsplit(g1_10,":"))
col10b <- data.frame(matrix(col10,ncol = len9,byrow = TRUE))
col10c <- col10b
names(col10c) <- names9
col11 <- unlist(strsplit(g1_11,":"))
col11b <- data.frame(matrix(col11,ncol = len9,byrow = TRUE))
col11c <- col11b
names(col11c) <- names9
id_t <- id_1
dfcol <- rbind(col10c)
dfcol3 <- rbind(col11c)
dfcol2 <- cbind(id_t,dfcol,dfcol3)
dfcol2 <- dfcol2[order(dfcol2$id_t),]
nnc <- ncol(dfcol2)
nnc2 <- (nnc-1) / 2
nnc3 <- nnc2 * 2 + 1
names(dfcol2)[(nnc2+2):nnc3]<- paste0("Tum_",names(dfcol2)[2:(nnc2+1)])
ad1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$DP4),",")),ncol = 4,byrow = TRUE))
names(ad1) <- c("Nor_Ref_ST_p","Nor_Ref_ST_n","Nor_Alt_ST_p","Nor_Alt_ST_n")
# gss1 <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT),",")),ncol = 4,byrow = TRUE))
# names(gss1) <- c("BCOUNT_ref","BCOUNT_alt","BCOUNT_3","BCOUNT_4")
ad1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$Tum_DP4),",")),ncol = 4,byrow = TRUE))
names(ad1b) <- c("Tum_Ref_ST_p","Tum_Ref_ST_n","Tum_Alt_ST_p","Tum_Alt_ST_n")
# gss1b <- data.frame(matrix(unlist(strsplit(as.character(dfcol2$BCOUNT_2),",")),ncol = 4,byrow = TRUE))
# names(gss1b) <- c("BCOUNT_ref_2","BCOUNT_alt_2","BCOUNT_2_3","BCOUNT_2_4")
# FINAL FORMAT
formatfin <- cbind(dfcol2[,c(1:7)],ad1,dfcol2[,c(9:14)],ad1b)
### INFO
f8 <- vcffile$V8
s1 <- tidyr::separate(data = vcffile, col = "V8", into = paste0("a",1:53), sep = ";")
s2 <- s1[,c(8,10:60)]
# s2 <- s2[,-2]
snames <- unlist(strsplit(as.character(s2[1,]),"="))
snames2 <- snames[c(seq(1,106,by = 2))]
azkeNA <- which(is.na(snames2))[1]-1
for(h in c(1:azkeNA))
{
print(h)
if(length(grep("GERP\\+\\+_RS", snames2[h]))>0)
{
s2[,h] <- gsub("GERP\\+\\+_RS","GERP_RS",s2[,h])
snames2[h] <- gsub("GERP\\+\\+_RS","GERP_RS",snames2[h])
}
s2[,h] <- gsub(paste0(snames2[h],"="),"",s2[,h])
names(s2)[h] <- snames2[h]
}
kendu <- sapply(s2,function(x)
{
nr <- length(x)
sr <- sum(is.na(x))
nr!=sr
})
tt <- table(kendu)
if(length(tt)>1) s2 <- s2[,kendu]
names(s2)[which(names(s2)=="DP")] <- "DP_Tum_Nor"
# names(s2)[42] <- "GERP"
# s2[,37] <- gsub(paste0("GERP++_RS=.","",s2[,h+1]))
dftot <- cbind(vcffile[,1:7],s2,formatfin)
names(dftot)[1:7] <- c("Chr","Pos","V3","Ref","Alt","V6","Filt")
names(dftot)[which(names(dftot)=="RD")] <- "Nor_Ref_D"
names(dftot)[which(names(dftot)=="DP")] <- "Nor_DP"
names(dftot)[which(names(dftot)=="AD")] <- "Nor_Alt_D"
names(dftot)[which(names(dftot)=="Tum_RD")] <- "Tum_Ref_D"
names(dftot)[which(names(dftot)=="Tum_AD")] <- "Tum_Alt_D"
w_names <- which(names(dftot)%in%c("Pos","DP_Tum_Nor","SSC","GPV","SPV","id_t","Nor_DP","Nor_Ref_D","Nor_Alt_D","Nor_Ref_ST_p" ,"Nor_Ref_ST_n", "Nor_Alt_ST_p", "Nor_Alt_ST_n",
"Tum_DP","Tum_Ref_D","Tum_Alt_D","Tum_Ref_ST_p","Tum_Ref_ST_n","Tum_Alt_ST_p","Tum_Alt_ST_n"))
for(z in w_names)
{
dftot[,z] <- as.numeric(as.character(dftot[,z]))
}
dftot$Tum_Ratio_Alt_st <- dftot$Tum_Alt_ST_p/dftot$Tum_Alt_ST_n
dftot$FREQ <- as.character(dftot$FREQ)
dftot$FREQ <- as.numeric(gsub("%","",dftot$FREQ))
dftot$Tum_FREQ <- as.character(dftot$Tum_FREQ)
dftot$Tum_FREQ <- as.numeric(gsub("%","",dftot$Tum_FREQ))
dftot$Tum_FREQ <- dftot$Tum_FREQ/100
dftot$FREQ <- dftot$FREQ/100
names(dftot)[which(names(dftot)=="FREQ")] <- "Nor_VAF"
names(dftot)[which(names(dftot)=="Tum_FREQ")] <- "Tum_VAF"
if(excel) openxlsx::write.xlsx(dftot, file = excel_file)
return(dftot)
}
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