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El
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@el-24188
Last seen 3.9 years 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