#' tardbpdms__load_toxicity
#'
#' Load variant toxicity estimates.
#'
#' @param dms_dir path to variant toxicity directory (required)
#' @param object load from R data object (default:F)
#' @param read_filter filter reads based on is.reads0 (default:T)
#'
#' @return a variant toxicity data.table
#' @export
tardbpdms__load_toxicity <- function(
dms_dir,
object=F,
read_filter=T
){
#Load variant toxicity data
if(object){
load(file.path(dms_dir, "DMS_processed_data.RData"))
silent = singles_silent[Nmut_aa==0]
singles = singles_silent[Nmut_aa==1]
}else{
silent <- data.table::fread(file.path(dms_dir, "DMS_silent.txt"))
singles <- data.table::fread(file.path(dms_dir, "DMS_singles.txt"))
doubles <- data.table::fread(file.path(dms_dir, "DMS_doubles.txt"))
}
#Toxicity - silent
for(i in names(silent)[grep("^fitness", names(silent))]){
j <- gsub('fitness','toxicity',i)
silent[, (j) := -.SD[[1]],,.SDcols = i]
}
#Toxicity - singles
for(i in names(singles)[grep("^fitness", names(singles))]){
j <- gsub('fitness','toxicity',i)
singles[, (j) := -.SD[[1]],,.SDcols = i]
}
#Toxicity - doubles
for(i in names(doubles)[grep("^fitness", names(doubles))]){
j <- gsub('fitness','toxicity',i)
doubles[, (j) := -.SD[[1]],,.SDcols = i]
}
#Combine
if(read_filter){
return(rbind(singles, silent, doubles, fill = T)[is.reads0==T,])
}else{
return(rbind(singles, silent, doubles, fill = T))
}
}
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