don't get an output of wigtoRangedData's function HMMcopy Package for detect CNV
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Entering edit mode
El • 0
@el-24188
Last seen 18 months ago

Enter the body of text here to illustrate, I have generated a script

Code should be placed in three backticks as shown below


wigToRangedData <- function(wigfile, verbose = TRUE) {
  if (verbose) { message(paste("Slurping:", wigfile)) }
  input <- readLines(readfile, warn = FALSE)
  breaks <- c(grep("fixedStep", input), length(input) + 1)
  temp <- NULL
  span <- NULL

  for (i in 1:(length(breaks) - 1)) {
    data_range <- (breaks[i] + 1):(breaks[i + 1] - 1)
    track_info <- input[breaks[i]]
    if (verbose) { message(paste("Parsing:", track_info)) }
    tokens <- strsplit(
      sub("fixedStep chrom=(\\S+) start=(\\d+) step=(\\d+) span=(\\d+)",
          "\\1 \\2 \\3 \\4", track_info, perl = TRUE), " ")[[1]]
    span <- as.integer(tokens[4])
    chr <- rep.int(tokens[1], length(data_range))
    pos <- seq(from = as.integer(tokens[2]), by = as.integer(tokens[3]),
               length.out = length(data_range))
    val <- as.numeric(input[data_range])
    temp <- c(temp, list(data.frame(chr, pos, val)))
  }
  if (verbose) { message("Sorting by decreasing chromosome size") }
  lengths <- as.integer(lapply(temp, nrow))
  temp <- temp[order(lengths, decreasing = TRUE)]
  temp = do.call("rbind", temp)
  output <- data.table(chr = temp$chr, start = temp$pos, end = temp$pos + span,
                       value = temp$val)
  return(output)
}


# Appeler une fonction
wigToRangedData("/Users/mac/Desktop/NGS-/ERR439247-pe.wig")

# Inspecter les resultas
head(output)



# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

I get > wigToRangedData("/Users/mac/Desktop/NGS-/ERR439247-pe.wig") Slurping: /Users/mac/Desktop/NGS-/ERR439247-pe.wig Error in (breaks[i] + 1):(breaks[i + 1] - 1) : NA/NaN argument

HMMcopy DNAcopy • 247 views
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