Nothing
R/filterread.r
In nanotatoR: nanotatoR: next generation structural variant annotation and classification
Defines functions
run_bionano_filter
Documented in
run_bionano_filter
#' Getting the data from annotated smaps to extract SV
#' information based on type of variants.
#'
#' @param input_fmt_geneList character. Choice of gene list input
#' Text or Dataframe.
#' @param input_fmt_svMap character. Choice of gene list input
#' Text or Dataframe.
#' @param SVFile character. SV file name.
#' @param svData Dataframe Input data containing SV data.
#' @param dat_geneList Dataframe Input data containing geneList data.
#' @param fileName Character Name of file containing Gene List data.
#' @param outpath Character Directory to the output file.
#' @param outputFilename Character Output filename.
#' @param RZIPpath Character Path for the Rtools Zip package.
#' @return Excel file containing the annotated SV map, tabs divided based on
#' type of SVs.
#' @examples
#' \dontrun{
#' terms <- "Muscle Weakness"
#' gene <- gene_list_generation(
#' method = "Single", term = terms,
#' returnMethod_GeneList = "dataFrame"
#' )
#' RzipFile = "zip.exe"
#' RZIPpath <- system.file("extdata", RzipFile, package = "nanotatoR")
#' smapName <- "F1.1_TestSample1_solo_hg19.smap"
#' smappath <- system.file("extdata", smapName, package = "nanotatoR")
#' smappath1 <- system.file("extdata", package = "nanotatoR")
#' run_bionano_filter(input_fmt_geneList = c("dataframe"), input_fmt_svMap = c("Text"),
#' SVFile = smappath, dat_geneList = gene, outpath = smappath1, outputFilename = "test",
#' RZIPpath = RZIPpath)
#' }
#' @import openxlsx
#' @import hash
#' @importFrom stats na.omit
#' @export
run_bionano_filter <- function(input_fmt_geneList = c("Text", "dataFrame"),
input_fmt_svMap = c("Text", "dataFrame"),
SVFile = NULL, svData, dat_geneList, fileName, outpath,
outputFilename = "", RZIPpath) {
# library(openxlsx)
# library(hash)
# setwd(path)##change the directory to your working directory
Sys.setenv("R_ZIPCMD" = RZIPpath)
## GeneList Input Format
if (input_fmt_geneList == "Text") {
rr <- read.table(fileName, header = TRUE)
}
else if (input_fmt_geneList == "dataFrame") {
rr <- dat_geneList
}
else {
stop("Dataframe Incorrect!!")
}
ha <- hash()
.set(ha, keys = rr$Genes, values = rr$Terms)
pg <- as.character(rr$Genes)
gen <- paste("^", pg, "$", sep = "")
# ll<-list.files(pattern="txt")
if (input_fmt_svMap == "Text") {
r <- read.table(SVFile, sep = "\t", header = TRUE)
}
else if (input_fmt_svMap == "dataFrame") {
r <- svData
}
else {
stop("Input Formats Incorrect")
}
ogene <- as.character(r$OverlapGenes_strand_perc)
upgene <- as.character(r$Upstream_nonOverlapGenes_dist_kb)
dngene <- as.character(r$Downstream_nonOverlapGenes_dist_kb)
# nogene<-c(upgene,dngene)
pagene <- c()
pagene_term <- c()
nopageneup <- c()
nopageneup_term <- c()
nopagenedn <- c()
nopagenedn_term <- c()
### OverlapGene
for (ii in seq_len(length(ogene))) {
dd <- grep(";", ogene[ii])
gene_Terms <- c()
if (length(dd) > 0) {
st <- strsplit(ogene[ii], ";")
gen2 <- as.character(unlist(st))
opag <- c()
for (l in seq_len(length(gen2))) {
st1 <- st <- strsplit(gen2[l], "\\(")
gen2[l] <- st1[[1]][1]
pa <- paste("^", gen2[l], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
opag <- c(opag, as.character(gen2[l]))
val1 <- hash::values(ha, keys = gen2[l])
gene_Terms <- c(gene_Terms, as.character(val1))
}
else {
opag <- c(opag, "-")
}
}
opag <- as.character(unique(opag))
opagt <- as.character(unique(gene_Terms))
opagt <- paste(opagt, collapse = ";")
if (length(opag) > 1) {
opagpa <- paste(opag, collapse = ";")
ff <- grep("-", opagpa)
if (length(ff) > 0) {
opagpa <- gsub("-", "", opagpa)
opagpa <- gsub(";;", ";", opagpa)
opagpa <- gsub("^;", "", opagpa)
pagene <- c(pagene, opagpa)
pagene_term <- c(pagene_term, opagt)
}
else {
pagene <- c(pagene, opagpa)
pagene_term <- c(pagene_term, opagt)
}
}
else {
pagene <- c(pagene, opag)
pagene_term <- c(pagene_term, opagt)
}
}
else {
st1 <- st <- strsplit(ogene[ii], "\\(")
ogene[ii] <- st1[[1]][1]
pa <- paste("^", ogene[ii], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
pagene <- c(pagene, as.character(ogene[ii]))
val1 <- hash::values(ha, keys = ogene[ii])
pagene_term <- c(pagene_term, as.character(val1))
}
else {
pagene <- c(pagene, "-")
pagene_term <- c(pagene_term, "-")
}
}
}
### Non-OverlapUpGene
for (jj in seq_len(length(upgene))) {
dd1 <- grep(";", upgene[jj])
gene_Terms_no <- c()
if (length(dd1) > 0) {
st1 <- strsplit(upgene[jj], ";")
gen3 <- as.character(unlist(st1))
nopag <- c()
for (l in seq_len(length(gen3))) {
st1 <- st <- strsplit(gen3[l], "\\(")
gen3[l] <- st1[[1]][1]
pa1 <- paste("^", gen3[l], "$", sep = "")
gg2 <- grep(pa1, gen, fixed = TRUE)
if (length(gg2) > 0) {
nopag <- c(nopag, as.character(gen3[l]))
val2 <- hash::values(ha, keys = gen3[l])
gene_Terms_no <- c(gene_Terms_no, as.character(val2))
}
else {
nopag <- c(nopag, "-")
}
}
nopag <- as.character(unique(nopag))
nopagt <- as.character(unique(gene_Terms_no))
nopagt <- paste(nopagt, collapse = ";")
if (length(nopag) > 1) {
nopagpa <- paste(nopag, collapse = ";")
ff <- grep("-", nopagpa)
if (length(ff) > 0) {
nopagpa <- gsub("-", "", nopagpa)
nopagpa <- gsub(";;", ";", nopagpa)
nopagpa <- gsub("^;", ";", nopagpa)
nopageneup <- c(nopageneup, nopagpa)
nopageneup_term <- c(nopageneup_term, nopagt)
}
else {
nopageneup <- c(nopageneup, nopagpa)
nopageneup_term <- c(nopageneup_term, nopagt)
}
}
else {
nopageneup <- c(nopageneup, nopag)
nopageneup_term <- c(nopageneup_term, nopagt)
}
}
else {
st1 <- st <- strsplit(upgene[ii], "\\(")
upgene[ii] <- st1[[1]][1]
pa <- paste("^", upgene[jj], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
nopageneup <- c(nopageneup, as.character(upgene[jj]))
val2 <- hash::values(ha, keys = upgene[jj])
nopageneup_term <- c(nopageneup_term, as.character(val2))
}
else {
nopageneup <- c(nopageneup, "-")
nopageneup_term <- c(nopageneup_term, "-")
}
}
}
### Non-OverlapDnGene
for (jj in seq_len(length(dngene))) {
dd1 <- grep(";", dngene[jj])
gene_Terms_no <- c()
if (length(dd1) > 0) {
st1 <- strsplit(dngene[jj], ";")
gen3 <- as.character(unlist(st1))
nopag <- c()
for (l in seq_len(length(gen3))) {
st1 <- st <- strsplit(gen3[l], "\\(")
gen3[l] <- st1[[1]][1]
pa1 <- paste("^", gen3[l], "$", sep = "")
gg2 <- grep(pa1, gen, fixed = TRUE)
if (length(gg2) > 0) {
nopag <- c(nopag, as.character(gen3[l]))
val2 <- hash::values(ha, keys = gen3[l])
gene_Terms_no <- c(gene_Terms_no, as.character(val2))
}
else {
nopag <- c(nopag, "-")
}
}
nopag <- as.character(unique(nopag))
nopagt <- as.character(unique(gene_Terms_no))
nopagt <- paste(nopagt, collapse = ";")
if (length(nopag) > 1) {
nopagpa <- paste(nopag, collapse = ";")
ff <- grep("-", nopagpa)
if (length(ff) > 0) {
nopagpa <- gsub("-", "", nopagpa)
nopagpa <- gsub(";;", ";", nopagpa)
nopagpa <- gsub("^;", ";", nopagpa)
nopagenedn <- c(nopagenedn, nopagpa)
nopagenedn_term <- c(nopagenedn_term, nopagt)
}
else {
nopagenedn <- c(nopagenedn, nopagpa)
nopagenedn_term <- c(nopagenedn_term, nopagt)
}
}
else {
nopagenedn <- c(nopagenedn, nopag)
nopagenedn_term <- c(nopagenedn_term, nopagt)
}
}
else {
st1 <- st <- strsplit(dngene[ii], "\\(")
dngene[ii] <- st1[[1]][1]
pa <- paste("^", dngene[jj], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
nopagenedn <- c(nopagenedn, as.character(dngene[jj]))
val2 <- hash::values(ha, keys = dngene[jj])
nopagenedn_term <- c(nopagenedn_term, as.character(val2))
}
else {
nopagenedn <- c(nopagenedn, "-")
nopagenedn_term <- c(nopagenedn_term, "-")
}
}
}
# len<-length(pagene)-length(pg)
# genesPG<-c(as.character(pg),rep("-",len))
data <- data.frame(cbind(
r, Overlap_PG = as.character(pagene),
Overlap_Terms = as.character(pagene_term),
Non_Overlap_UP_PG = as.character(nopageneup),
Non_Overlap_UP_Terms = as.character(nopageneup_term),
Non_Overlap_DN_PG = as.character(nopagenedn),
Non_Overlap_DN_Terms = as.character(nopagenedn_term)
))
data$BNG_Freq_Perc_Filtered<-gsub("-",0,as.character(data$BNG_Freq_Perc_Filtered))
data$BNG_Freq_Perc_UnFiltered<-gsub("-",0,as.character(
data$BNG_Freq_Perc_UnFiltered))
data$DGV_Freq_Perc<-as.numeric(data$DGV_Freq_Perc)
data$Internal_Freq_Perc_Filtered<-as.numeric(
data$Internal_Freq_Perc_Filtered)
data$Internal_Freq_Perc_Unfiltered<-as.numeric(
data$Internal_Freq_Perc_Unfiltered)
data$BNG_Freq_Perc_Filtered<-as.numeric(data$BNG_Freq_Perc_Filtered)
data$BNG_Freq_Perc_UnFiltered<-as.numeric(data$BNG_Freq_Perc_UnFiltered)
data$DECIPHER_Frequency<-as.numeric(data$DECIPHER_Frequency)
data$Type1<-as.character(data$Type1)
data$Type2<-as.character(data$Type2)
dat <- data[which(data$Type %in% "insertion"), ]
dat1 <- data[which(data$Type %in% "deletion"), ]
dat44 <- data[which(data$Type %in% "duplication"), ]
dat45 <- data[which(data$Type %in% "duplication_split"), ]
dat46 <- data[which(data$Type %in% "duplication_inverted"), ]
dat_dup_rem<-rbind(dat44,dat45,dat46)
dat_dup_rem_FINAL<-dat_dup_rem[which(((dat_dup_rem$Type %in% "duplication") |
(
dat_dup_rem$Type %in% "duplication_split") |
(dat_dup_rem$Type %in% "duplication_inverted"))&
(((dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "fail" &
dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "-" &
dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")))), ]
dat3 <- rbind(dat1, dat, dat_dup_rem_FINAL)
dat10 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "none") |
(dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "-") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "none"))), ]
dat11 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "both") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "both") |
(dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "-") |
(dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "mother") |
(dat3$Found_in_parents_BSPQI_molecules == "mother" &
dat3$Found_in_parents_BSSSI_molecules == "both") |
(dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "father") |
(dat3$Found_in_parents_BSPQI_molecules == "father" &
dat3$Found_in_parents_BSSSI_molecules == "both"))),]
dat12 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "mother" &
dat3$Found_in_parents_BSSSI_molecules == "mother") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "mother") |
(dat3$Found_in_parents_BSPQI_molecules == "mother" &
dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat13 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "father" &
dat3$Found_in_parents_BSSSI_molecules == "father") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "father") |
(dat3$Found_in_parents_BSPQI_molecules == "father" &
dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat14 <- rbind(dat11, dat12, dat13)
gg <- grep("inversion", as.character(data$Type))
dat8 <- data[gg, ]
dat8 <- dat8[which(((dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "yes") |
(dat8$Found_in_self_BSPQI_molecules == "no" &
dat8$Found_in_self_BSSSI_molecules == "yes") |
(dat8$Found_in_self_BSPQI_molecules == "yes" &
dat8$Found_in_self_BSSSI_molecules == "no") |
(dat8$Found_in_self_BSPQI_molecules == "yes" &
dat8$Found_in_self_BSSSI_molecules == "-") |
(dat8$Found_in_self_BSPQI_molecules == "-" &
dat8$Found_in_self_BSSSI_molecules == "yes")) &
((dat8$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat8$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat8$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat8$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat8$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "-" &
dat8$Fail_BSSSI_assembly_chimeric_score == "pass"))), ]
gg1 <- grep("translocation", as.character(data$Type))
dat7 <- data[gg1, ]
dat7 <- dat7[which(((dat7$Found_in_self_BSPQI_molecules == "yes" &
dat7$Found_in_self_BSSSI_molecules == "yes") |
(dat7$Found_in_self_BSPQI_molecules == "no" &
dat7$Found_in_self_BSSSI_molecules == "yes") |
(dat7$Found_in_self_BSPQI_molecules == "yes" &
dat7$Found_in_self_BSSSI_molecules == "no") |
(dat7$Found_in_self_BSPQI_molecules == "yes" &
dat7$Found_in_self_BSSSI_molecules == "-") |
(dat7$Found_in_self_BSPQI_molecules == "-" &
dat7$Found_in_self_BSSSI_molecules == "yes")) &
((dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat7$Fail_BSPQI_assembly_chimeric_score == "fail" &
dat7$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat7$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat7$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "-" &
dat7$Fail_BSSSI_assembly_chimeric_score == "pass"))), ]
dat6 <- data[which(data$Type %in% "MisMatch"), ]
dat14 <- rbind(dat11, dat12, dat13)
ovrlapPG<-which(!((as.character(data$Overlap_PG)=="-")))
datovrlapPG<-data[ovrlapPG,]
nonovrlapupPG<-which(!((as.character(data$Non_Overlap_UP_PG)=="-")))
datnonovrlapUPPG<-data[nonovrlapupPG,]
nonovrlapdnPG<-which(!((as.character(data$Non_Overlap_DN_PG)=="-")))
datnonovrlapDNPG<-data[nonovrlapdnPG,]
list_of_datasets <- list(
"all" = data, "indel_dup_denovo" = dat10,
"indel_dup_both" = dat11,
"indel_dup_mother" = dat12, "indel_dup_father" = dat13,
"indel_dup_cmpdHET" = dat14, "inv" = dat8, "trans" = dat7,
"mismatch" = dat6,
"all_PG_OV" = datovrlapPG)
# gg<-grep("inversion",as.character(data$Type))
# dat8<-data[gg,]
# gg1<-grep("translocation",as.character(data$Type))
# dat7<-data[gg1,]
# dat6<-data[which(data$Type %in% "MisMatch"),]
# list_of_datasets <- list("all" = data, "indel" = dat3, "indel_denovo"= dat10, "indel_both"= dat11,
# "indel_mother"= dat12, "indel father"= dat13, "indel_cmpdHET"=dat14, "inv"= dat8, "trans"=dat7, "mismatch"=dat6,
# "all_PG_OV"=data, "all_PG_Non_OV"= data)
# st1<-strsplit(SVFile,".txt")[[1]][1]
fname <- paste(outputFilename, ".xlsx", sep = "")
write.xlsx(list_of_datasets, file = file.path(outpath, fname),keepNA=TRUE)
}
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Defines functions run_bionano_filter
Documented in run_bionano_filter
#' Getting the data from annotated smaps to extract SV
#' information based on type of variants.
#'
#' @param input_fmt_geneList character. Choice of gene list input
#' Text or Dataframe.
#' @param input_fmt_svMap character. Choice of gene list input
#' Text or Dataframe.
#' @param SVFile character. SV file name.
#' @param svData Dataframe Input data containing SV data.
#' @param dat_geneList Dataframe Input data containing geneList data.
#' @param fileName Character Name of file containing Gene List data.
#' @param outpath Character Directory to the output file.
#' @param outputFilename Character Output filename.
#' @param RZIPpath Character Path for the Rtools Zip package.
#' @return Excel file containing the annotated SV map, tabs divided based on
#' type of SVs.
#' @examples
#' \dontrun{
#' terms <- "Muscle Weakness"
#' gene <- gene_list_generation(
#' method = "Single", term = terms,
#' returnMethod_GeneList = "dataFrame"
#' )
#' RzipFile = "zip.exe"
#' RZIPpath <- system.file("extdata", RzipFile, package = "nanotatoR")
#' smapName <- "F1.1_TestSample1_solo_hg19.smap"
#' smappath <- system.file("extdata", smapName, package = "nanotatoR")
#' smappath1 <- system.file("extdata", package = "nanotatoR")
#' run_bionano_filter(input_fmt_geneList = c("dataframe"), input_fmt_svMap = c("Text"),
#' SVFile = smappath, dat_geneList = gene, outpath = smappath1, outputFilename = "test",
#' RZIPpath = RZIPpath)
#' }
#' @import openxlsx
#' @import hash
#' @importFrom stats na.omit
#' @export
run_bionano_filter <- function(input_fmt_geneList = c("Text", "dataFrame"),
input_fmt_svMap = c("Text", "dataFrame"),
SVFile = NULL, svData, dat_geneList, fileName, outpath,
outputFilename = "", RZIPpath) {
# library(openxlsx)
# library(hash)
# setwd(path)##change the directory to your working directory
Sys.setenv("R_ZIPCMD" = RZIPpath)
## GeneList Input Format
if (input_fmt_geneList == "Text") {
rr <- read.table(fileName, header = TRUE)
}
else if (input_fmt_geneList == "dataFrame") {
rr <- dat_geneList
}
else {
stop("Dataframe Incorrect!!")
}
ha <- hash()
.set(ha, keys = rr$Genes, values = rr$Terms)
pg <- as.character(rr$Genes)
gen <- paste("^", pg, "$", sep = "")
# ll<-list.files(pattern="txt")
if (input_fmt_svMap == "Text") {
r <- read.table(SVFile, sep = "\t", header = TRUE)
}
else if (input_fmt_svMap == "dataFrame") {
r <- svData
}
else {
stop("Input Formats Incorrect")
}
ogene <- as.character(r$OverlapGenes_strand_perc)
upgene <- as.character(r$Upstream_nonOverlapGenes_dist_kb)
dngene <- as.character(r$Downstream_nonOverlapGenes_dist_kb)
# nogene<-c(upgene,dngene)
pagene <- c()
pagene_term <- c()
nopageneup <- c()
nopageneup_term <- c()
nopagenedn <- c()
nopagenedn_term <- c()
### OverlapGene
for (ii in seq_len(length(ogene))) {
dd <- grep(";", ogene[ii])
gene_Terms <- c()
if (length(dd) > 0) {
st <- strsplit(ogene[ii], ";")
gen2 <- as.character(unlist(st))
opag <- c()
for (l in seq_len(length(gen2))) {
st1 <- st <- strsplit(gen2[l], "\\(")
gen2[l] <- st1[[1]][1]
pa <- paste("^", gen2[l], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
opag <- c(opag, as.character(gen2[l]))
val1 <- hash::values(ha, keys = gen2[l])
gene_Terms <- c(gene_Terms, as.character(val1))
}
else {
opag <- c(opag, "-")
}
}
opag <- as.character(unique(opag))
opagt <- as.character(unique(gene_Terms))
opagt <- paste(opagt, collapse = ";")
if (length(opag) > 1) {
opagpa <- paste(opag, collapse = ";")
ff <- grep("-", opagpa)
if (length(ff) > 0) {
opagpa <- gsub("-", "", opagpa)
opagpa <- gsub(";;", ";", opagpa)
opagpa <- gsub("^;", "", opagpa)
pagene <- c(pagene, opagpa)
pagene_term <- c(pagene_term, opagt)
}
else {
pagene <- c(pagene, opagpa)
pagene_term <- c(pagene_term, opagt)
}
}
else {
pagene <- c(pagene, opag)
pagene_term <- c(pagene_term, opagt)
}
}
else {
st1 <- st <- strsplit(ogene[ii], "\\(")
ogene[ii] <- st1[[1]][1]
pa <- paste("^", ogene[ii], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
pagene <- c(pagene, as.character(ogene[ii]))
val1 <- hash::values(ha, keys = ogene[ii])
pagene_term <- c(pagene_term, as.character(val1))
}
else {
pagene <- c(pagene, "-")
pagene_term <- c(pagene_term, "-")
}
}
}
### Non-OverlapUpGene
for (jj in seq_len(length(upgene))) {
dd1 <- grep(";", upgene[jj])
gene_Terms_no <- c()
if (length(dd1) > 0) {
st1 <- strsplit(upgene[jj], ";")
gen3 <- as.character(unlist(st1))
nopag <- c()
for (l in seq_len(length(gen3))) {
st1 <- st <- strsplit(gen3[l], "\\(")
gen3[l] <- st1[[1]][1]
pa1 <- paste("^", gen3[l], "$", sep = "")
gg2 <- grep(pa1, gen, fixed = TRUE)
if (length(gg2) > 0) {
nopag <- c(nopag, as.character(gen3[l]))
val2 <- hash::values(ha, keys = gen3[l])
gene_Terms_no <- c(gene_Terms_no, as.character(val2))
}
else {
nopag <- c(nopag, "-")
}
}
nopag <- as.character(unique(nopag))
nopagt <- as.character(unique(gene_Terms_no))
nopagt <- paste(nopagt, collapse = ";")
if (length(nopag) > 1) {
nopagpa <- paste(nopag, collapse = ";")
ff <- grep("-", nopagpa)
if (length(ff) > 0) {
nopagpa <- gsub("-", "", nopagpa)
nopagpa <- gsub(";;", ";", nopagpa)
nopagpa <- gsub("^;", ";", nopagpa)
nopageneup <- c(nopageneup, nopagpa)
nopageneup_term <- c(nopageneup_term, nopagt)
}
else {
nopageneup <- c(nopageneup, nopagpa)
nopageneup_term <- c(nopageneup_term, nopagt)
}
}
else {
nopageneup <- c(nopageneup, nopag)
nopageneup_term <- c(nopageneup_term, nopagt)
}
}
else {
st1 <- st <- strsplit(upgene[ii], "\\(")
upgene[ii] <- st1[[1]][1]
pa <- paste("^", upgene[jj], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
nopageneup <- c(nopageneup, as.character(upgene[jj]))
val2 <- hash::values(ha, keys = upgene[jj])
nopageneup_term <- c(nopageneup_term, as.character(val2))
}
else {
nopageneup <- c(nopageneup, "-")
nopageneup_term <- c(nopageneup_term, "-")
}
}
}
### Non-OverlapDnGene
for (jj in seq_len(length(dngene))) {
dd1 <- grep(";", dngene[jj])
gene_Terms_no <- c()
if (length(dd1) > 0) {
st1 <- strsplit(dngene[jj], ";")
gen3 <- as.character(unlist(st1))
nopag <- c()
for (l in seq_len(length(gen3))) {
st1 <- st <- strsplit(gen3[l], "\\(")
gen3[l] <- st1[[1]][1]
pa1 <- paste("^", gen3[l], "$", sep = "")
gg2 <- grep(pa1, gen, fixed = TRUE)
if (length(gg2) > 0) {
nopag <- c(nopag, as.character(gen3[l]))
val2 <- hash::values(ha, keys = gen3[l])
gene_Terms_no <- c(gene_Terms_no, as.character(val2))
}
else {
nopag <- c(nopag, "-")
}
}
nopag <- as.character(unique(nopag))
nopagt <- as.character(unique(gene_Terms_no))
nopagt <- paste(nopagt, collapse = ";")
if (length(nopag) > 1) {
nopagpa <- paste(nopag, collapse = ";")
ff <- grep("-", nopagpa)
if (length(ff) > 0) {
nopagpa <- gsub("-", "", nopagpa)
nopagpa <- gsub(";;", ";", nopagpa)
nopagpa <- gsub("^;", ";", nopagpa)
nopagenedn <- c(nopagenedn, nopagpa)
nopagenedn_term <- c(nopagenedn_term, nopagt)
}
else {
nopagenedn <- c(nopagenedn, nopagpa)
nopagenedn_term <- c(nopagenedn_term, nopagt)
}
}
else {
nopagenedn <- c(nopagenedn, nopag)
nopagenedn_term <- c(nopagenedn_term, nopagt)
}
}
else {
st1 <- st <- strsplit(dngene[ii], "\\(")
dngene[ii] <- st1[[1]][1]
pa <- paste("^", dngene[jj], "$", sep = "")
gg <- grep(pa, gen, fixed = TRUE)
if (length(gg) > 0) {
nopagenedn <- c(nopagenedn, as.character(dngene[jj]))
val2 <- hash::values(ha, keys = dngene[jj])
nopagenedn_term <- c(nopagenedn_term, as.character(val2))
}
else {
nopagenedn <- c(nopagenedn, "-")
nopagenedn_term <- c(nopagenedn_term, "-")
}
}
}
# len<-length(pagene)-length(pg)
# genesPG<-c(as.character(pg),rep("-",len))
data <- data.frame(cbind(
r, Overlap_PG = as.character(pagene),
Overlap_Terms = as.character(pagene_term),
Non_Overlap_UP_PG = as.character(nopageneup),
Non_Overlap_UP_Terms = as.character(nopageneup_term),
Non_Overlap_DN_PG = as.character(nopagenedn),
Non_Overlap_DN_Terms = as.character(nopagenedn_term)
))
data$BNG_Freq_Perc_Filtered<-gsub("-",0,as.character(data$BNG_Freq_Perc_Filtered))
data$BNG_Freq_Perc_UnFiltered<-gsub("-",0,as.character(
data$BNG_Freq_Perc_UnFiltered))
data$DGV_Freq_Perc<-as.numeric(data$DGV_Freq_Perc)
data$Internal_Freq_Perc_Filtered<-as.numeric(
data$Internal_Freq_Perc_Filtered)
data$Internal_Freq_Perc_Unfiltered<-as.numeric(
data$Internal_Freq_Perc_Unfiltered)
data$BNG_Freq_Perc_Filtered<-as.numeric(data$BNG_Freq_Perc_Filtered)
data$BNG_Freq_Perc_UnFiltered<-as.numeric(data$BNG_Freq_Perc_UnFiltered)
data$DECIPHER_Frequency<-as.numeric(data$DECIPHER_Frequency)
data$Type1<-as.character(data$Type1)
data$Type2<-as.character(data$Type2)
dat <- data[which(data$Type %in% "insertion"), ]
dat1 <- data[which(data$Type %in% "deletion"), ]
dat44 <- data[which(data$Type %in% "duplication"), ]
dat45 <- data[which(data$Type %in% "duplication_split"), ]
dat46 <- data[which(data$Type %in% "duplication_inverted"), ]
dat_dup_rem<-rbind(dat44,dat45,dat46)
dat_dup_rem_FINAL<-dat_dup_rem[which(((dat_dup_rem$Type %in% "duplication") |
(
dat_dup_rem$Type %in% "duplication_split") |
(dat_dup_rem$Type %in% "duplication_inverted"))&
(((dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "fail" &
dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat_dup_rem$Fail_BSPQI_assembly_chimeric_score == "-" &
dat_dup_rem$Fail_BSSSI_assembly_chimeric_score == "pass")))), ]
dat3 <- rbind(dat1, dat, dat_dup_rem_FINAL)
dat10 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no"
& dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes"
& dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "none") |
(dat3$Found_in_parents_BSPQI_molecules == "none"
& dat3$Found_in_parents_BSSSI_molecules == "-") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "none"))), ]
dat11 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "both") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "both") |
(dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "-") |
(dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "mother") |
(dat3$Found_in_parents_BSPQI_molecules == "mother" &
dat3$Found_in_parents_BSSSI_molecules == "both") |
(dat3$Found_in_parents_BSPQI_molecules == "both" &
dat3$Found_in_parents_BSSSI_molecules == "father") |
(dat3$Found_in_parents_BSPQI_molecules == "father" &
dat3$Found_in_parents_BSSSI_molecules == "both"))),]
dat12 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "mother" &
dat3$Found_in_parents_BSSSI_molecules == "mother") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "mother") |
(dat3$Found_in_parents_BSPQI_molecules == "mother" &
dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat13 <- dat3[which(((dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "no" &
dat3$Found_in_self_BSSSI_molecules == "yes") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "no") |
(dat3$Found_in_self_BSPQI_molecules == "yes" &
dat3$Found_in_self_BSSSI_molecules == "-") |
(dat3$Found_in_self_BSPQI_molecules == "-" &
dat3$Found_in_self_BSSSI_molecules == "yes")) &
((dat3$Found_in_parents_BSPQI_molecules == "father" &
dat3$Found_in_parents_BSSSI_molecules == "father") |
(dat3$Found_in_parents_BSPQI_molecules == "-" &
dat3$Found_in_parents_BSSSI_molecules == "father") |
(dat3$Found_in_parents_BSPQI_molecules == "father" &
dat3$Found_in_parents_BSSSI_molecules == "-"))), ]
dat14 <- rbind(dat11, dat12, dat13)
gg <- grep("inversion", as.character(data$Type))
dat8 <- data[gg, ]
dat8 <- dat8[which(((dat8$Found_in_self_BSPQI_molecules == "yes"
& dat8$Found_in_self_BSSSI_molecules == "yes") |
(dat8$Found_in_self_BSPQI_molecules == "no" &
dat8$Found_in_self_BSSSI_molecules == "yes") |
(dat8$Found_in_self_BSPQI_molecules == "yes" &
dat8$Found_in_self_BSSSI_molecules == "no") |
(dat8$Found_in_self_BSPQI_molecules == "yes" &
dat8$Found_in_self_BSSSI_molecules == "-") |
(dat8$Found_in_self_BSPQI_molecules == "-" &
dat8$Found_in_self_BSSSI_molecules == "yes")) &
((dat8$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat8$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat8$Fail_BSPQI_assembly_chimeric_score == "fail"
& dat8$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat8$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat8$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat8$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat8$Fail_BSPQI_assembly_chimeric_score == "-" &
dat8$Fail_BSSSI_assembly_chimeric_score == "pass"))), ]
gg1 <- grep("translocation", as.character(data$Type))
dat7 <- data[gg1, ]
dat7 <- dat7[which(((dat7$Found_in_self_BSPQI_molecules == "yes" &
dat7$Found_in_self_BSSSI_molecules == "yes") |
(dat7$Found_in_self_BSPQI_molecules == "no" &
dat7$Found_in_self_BSSSI_molecules == "yes") |
(dat7$Found_in_self_BSPQI_molecules == "yes" &
dat7$Found_in_self_BSSSI_molecules == "no") |
(dat7$Found_in_self_BSPQI_molecules == "yes" &
dat7$Found_in_self_BSSSI_molecules == "-") |
(dat7$Found_in_self_BSPQI_molecules == "-" &
dat7$Found_in_self_BSSSI_molecules == "yes")) &
((dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat7$Fail_BSPQI_assembly_chimeric_score == "fail" &
dat7$Fail_BSSSI_assembly_chimeric_score == "pass") |
(dat7$Fail_BSPQI_assembly_chimeric_score == "pass" &
dat7$Fail_BSSSI_assembly_chimeric_score == "fail")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "pass"
& dat7$Fail_BSSSI_assembly_chimeric_score == "-")
| (dat7$Fail_BSPQI_assembly_chimeric_score == "-" &
dat7$Fail_BSSSI_assembly_chimeric_score == "pass"))), ]
dat6 <- data[which(data$Type %in% "MisMatch"), ]
dat14 <- rbind(dat11, dat12, dat13)
ovrlapPG<-which(!((as.character(data$Overlap_PG)=="-")))
datovrlapPG<-data[ovrlapPG,]
nonovrlapupPG<-which(!((as.character(data$Non_Overlap_UP_PG)=="-")))
datnonovrlapUPPG<-data[nonovrlapupPG,]
nonovrlapdnPG<-which(!((as.character(data$Non_Overlap_DN_PG)=="-")))
datnonovrlapDNPG<-data[nonovrlapdnPG,]
list_of_datasets <- list(
"all" = data, "indel_dup_denovo" = dat10,
"indel_dup_both" = dat11,
"indel_dup_mother" = dat12, "indel_dup_father" = dat13,
"indel_dup_cmpdHET" = dat14, "inv" = dat8, "trans" = dat7,
"mismatch" = dat6,
"all_PG_OV" = datovrlapPG)
# gg<-grep("inversion",as.character(data$Type))
# dat8<-data[gg,]
# gg1<-grep("translocation",as.character(data$Type))
# dat7<-data[gg1,]
# dat6<-data[which(data$Type %in% "MisMatch"),]
# list_of_datasets <- list("all" = data, "indel" = dat3, "indel_denovo"= dat10, "indel_both"= dat11,
# "indel_mother"= dat12, "indel father"= dat13, "indel_cmpdHET"=dat14, "inv"= dat8, "trans"=dat7, "mismatch"=dat6,
# "all_PG_OV"=data, "all_PG_Non_OV"= data)
# st1<-strsplit(SVFile,".txt")[[1]][1]
fname <- paste(outputFilename, ".xlsx", sep = "")
write.xlsx(list_of_datasets, file = file.path(outpath, fname),keepNA=TRUE)
}
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