+|
+```{r}
+#| echo: false
+#| results: "asis"
+#| out.extra: 'class="equal-size-img"'
+if (file.exists("off_targets.png")) {
+ knitr::include_graphics("off_targets.png")
+} else {
+ cat(' Off Target Sites not available ')
+}
+```
+ |
+
```{r}
#| echo: false
#| results: 'asis'
off_target_df <- as.data.frame(report_data$tables$off_target_indels)
if (is.data.frame(off_target_df) && nrow(off_target_df) > 0) {
- is_target_col_name <- if("is_target" %in% colnames(off_target_df)) "is_target" else "is_target_site"
-
- if(is_target_col_name %in% colnames(off_target_df)) {
- off_target_df[[is_target_col_name]] <- as.character(off_target_df[[is_target_col_name]])
+ if("is_target" %in% colnames(off_target_df)) {
+ off_target_df$is_target <- as.character(off_target_df$is_target)
} else {
- off_target_df[[is_target_col_name]] <- '0'
- }
-
- on_target_sites <- off_target_df[off_target_df[[is_target_col_name]] == '1', ]
- potential_off_targets <- off_target_df[off_target_df[[is_target_col_name]] == '0', ]
-
- is_proximal_to_on_target <- function(chrom, start, on_targets) {
- if(nrow(on_targets) == 0) return(FALSE)
- same_chrom_on_targets <- on_targets[on_targets$chrom == chrom, ]
- if(nrow(same_chrom_on_targets) == 0) return(FALSE)
- min_dist <- min(abs(as.numeric(same_chrom_on_targets$start) - as.numeric(start)))
- return(min_dist <= 3)
- }
-
- if (nrow(potential_off_targets) > 0 && nrow(on_target_sites) > 0) {
- proximal_mask <- mapply(is_proximal_to_on_target,
- potential_off_targets$chrom,
- potential_off_targets$start,
- MoreArgs = list(on_targets = on_target_sites))
- true_off_targets <- potential_off_targets[!proximal_mask, ]
- } else {
- true_off_targets <- potential_off_targets
+ off_target_df$is_target <- '0'
}
- off_target_filtered <- true_off_targets[
- as.numeric(true_off_targets$indel_fraction) * 100 > as.numeric(params$off_target_threshold),
+ potential_off_targets <- off_target_df[off_target_df$is_target == '0', ]
+
+ # Filter by threshold
+ off_target_filtered <- potential_off_targets[
+ as.numeric(potential_off_targets$indel_fraction) * 100 > off_target_threshold_value,
]
if(nrow(off_target_filtered) > 0){
- cat('')
- cat("| Genome Coordinate | % Indels | Annotation |
|---|
")
+ cat('\n')
+ cat("| Genome Coordinate | % Indels | Annotation |
|---|
\n")
for(i in 1:nrow(off_target_filtered)){
coord <- paste0(off_target_filtered[i, "chrom"], ":", off_target_filtered[i, "start"])
indels <- paste0(round(as.numeric(off_target_filtered[i, "indel_fraction"]) * 100, 1), "%")
- annotation <- off_target_filtered[i, "Annotation"]
- cat(paste0("| ", coord, " | ", indels, " | ", annotation, " | "))
+
+ raw_annotation <- off_target_filtered[i, "target_info"]
+ annotation <- raw_annotation
+
+ # Parse Annotation
+ if (!is.na(raw_annotation) && raw_annotation != "" && raw_annotation != ".") {
+ parts <- strsplit(raw_annotation, ";")[[1]]
+ csq_part <- parts[grep("^CSQ=", parts)]
+ if(length(csq_part) > 0) {
+ csq_val <- sub("^CSQ=", "", csq_part[1])
+ transcripts <- strsplit(csq_val, ",")[[1]]
+ t1 <- transcripts[1]
+ fields <- strsplit(t1, "\\|")[[1]]
+ # Assuming SYMBOL|Gene|Consequence|... based on observed VEP output
+ # ANNOTATE_OFFTARGETS specifies --fields "SYMBOL,Gene,Consequence,..."
+ # We found index 1 is Symbol, index 2 is Gene ID, index 3 is Consequence
+ if (length(fields) >= 3) {
+ gene_sym <- fields[1]
+ cons <- fields[3]
+ if (gene_sym == "") gene_sym <- fields[2]
+ if (gene_sym == "") gene_sym <- "N/A"
+ # Replace '&' with '
' in consequence string for better readability
+ cons <- gsub("&", "
", cons)
+ annotation <- paste0("Gene: ", gene_sym, "
Consequence: ", cons)
+ }
+ }
+ }
+
+ cat(paste0("| ", coord, " | ", indels, " | ", annotation, " | \n"))
}
- cat(" ")
+ cat(" \n")
} else {
- cat(paste0("No off-target sites with > ", off_target_threshold_value, "% indel frequency found. "))
+ cat(paste0("No off-target sites with > ", off_target_threshold_value, "% indel frequency found. \n"))
}
} else {
- cat(paste0("No off-target sites with > ", off_target_threshold_value, "% indel frequency found. "))
+ cat(paste0("No off-target sites with > ", off_target_threshold_value, "% indel frequency found. \n"))
}
```
- |
+
+
+ 
+