Project: s41467-025-59653-x | Function: CalcEditR (r)

system: You are an expert R programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow R best practices and maintain consistent code style.
Return **only** the complete R function code.

user: Complete this R function:

**DESCRIPTION:** Calculate CRISPR editing efficiency and analyze editing patterns across guide RNA sequences. Processes sequencing data to quantify editing outcomes.

**KEY TERMS:** {
  "guideseq": "guide RNA sequence",
  "p.val.cutoff": "statistical significance threshold",
  "editing efficiency": "fraction of edited reads"
}

**CONTEXT CODE:**   sangs.plot <- sangs %>% dplyr::select(index, base.call) 
  sangs.plot %<>% left_join(signal.noise.df)
  sangs.plot$type <- ordered(sangs.plot$type, levels = c("signal", "noise"))
  
  rolling_sang_percent <- sangs.plot %>% filter(measure == "perc", type == "noise") %>% dplyr::mutate(percent_3 = zoo::rollmean(value, k = 2, fill = NA)) %>% filter(percent_3 > percent_noise)
  
  peak_5 <- rolling_sang_percent %>% filter(index < guide.coord$start) %>% tail(n=1)
  peak_3 <- rolling_sang_percent %>% filter(index > guide.coord$end) %>% head(n=1)
  
  trim_left <- 20 # default start with 20 
  trim_right <- tail(sangs.plot, n=1)$index
  if (nrow(peak_5) > 0) {
    trim_left <- max(trim_left, peak_5$index)
  }
  if (nrow(peak_3) > 0) {
    trim_right <- peak_3$index
  }
  if ((trim_right - trim_left) < 100) {
    stop("Distance between autocalculated 5' trim and 3' trim location is less than 100 nucleotides. Read quality could be low, or alignmnet of the guide to the sequence might have been bad")
  }
  return(list(trim5 = trim_left, trim3 = trim_right))
}

CreateEditingSpread <- function(editing.df) {
  # Originally in server.R
  ### Reshape data
  edit.long <- editing.df %>% gather(key = focal.base, value = value, 
                                     A.area:T.area, A.perc:T.perc, T.pval:A.pval) %>%
    separate(col = focal.base, into = c("focal.base", "measure"))
  
  edit.spread <- edit.long %>% 
    spread(key = measure, value = value) 
}

CreateAvgBase <- function(sangs.filt) {
  #### Repeat code for getting avg.base from base.infoReactive
  # finding the average percent signal for each base
  sangs.filt %>% gather(key = focal.base, value = value, 
                        A.area:T.area, A.perc:T.perc) %>%
    separate(col = focal.base, into = c("focal.base", "measure")) %>% 
    spread(key = measure, value = value) %>% 
    filter(base.call == focal.base) %>% 
    group_by(focal.base) %>% 
    summarize(avg.percsignal = mean(perc),
              avg.areasignal = mean(area))
}

library(tidyverse)
library(zoo)

CalcEditR <- function(filename, guideseq, p.val.cutoff, default.trim, is.reverse) {
  stop("Function implementation has been masked")
}

CreateEditingSpread <- function(editing.df) {
  # Reshape data
  edit.long <- editing.df %>%
    gather(key = focal.base, value = value, 
           A.area:T.area, A.perc:T.perc, T.pval:A.pval) %>%
    separate(col = focal.base, into = c("focal.base", "measure"))

  edit.spread <- edit.long %>% 
    spread(key = measure, value = value) 

  return(edit.spread)
}

CreateAvgBase <- function(sangs.filt) {
  # finding the average percent signal for each base
  avg.base <- sangs.filt %>% 
    gather(key = focal.base, value = value, 
           A.area:T.area, A.perc:T.perc) %>%
    separate(col = focal.base, into = c("focal.base", "measure")) %>% 
    spread(key = measure, value = value) %>% 
    filter(base.call == focal.base) %>% 
    group_by(focal.base) %>% 
    summarize(avg.percsignal = mean(perc),
              avg.areasignal = mean(area))

  return(avg.base)
}

CalcEditRBatch <- function(file.id, filenames, datapaths, guideseq, reverseYN) {
  p.val.cutoff <- 0.01
  default.trim <- FALSE
  is.reverse <- (reverseYN == "Y")
  file.matches <- grepl(paste0("^", file.id, "_"), filenames)
  if (sum(file.matches) != 1) {
    stop(paste("The provided file ID", file.id, "matched multiple files in the directory or could not be found"))
  }
  filename <- datapaths[file.matches]
  
  results <- CalcEditR(filename, guideseq, p.val.cutoff, default.trim, is.reverse)
  results
}


Complete the function implementation replacing "stop("Not implemented")".