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Removed defunct functions and arguments.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,122 +1,11 @@ | ||
| #' Calculate interval weights | ||
| #' | ||
| #' Creates an interval weight file useful for segmentation. Requires a set of | ||
| #' coverage files from normal samples. Interval weights will be | ||
| #' set proportional to the inverse of coverage standard deviation across all | ||
| #' normals. Intervals with high variance in coverage in the pool of normals are | ||
| #' thus down-weighted. | ||
| #' | ||
| #' This function is now automatically called by \code{\link{createNormalDatabase}} | ||
| #' and is thus deprecated. | ||
| #' and is thus defunct. | ||
| #' | ||
| #' @param normalDB Database of normal samples, created with | ||
| #' \code{\link{createNormalDatabase}}. | ||
| #' @param interval.weight.file Output filename. | ||
| #' @param top.quantile Cap weight at the specified quantile. Intervals | ||
| #' with standard deviation smaller than this value won't have a higher weight | ||
| #' than intervals at this quantile. | ||
| #' @param plot Diagnostics plot, useful to tune parameters. | ||
| #' @param normal.coverage.files Deprecated. | ||
| #' @return A normalDB object with following slots added | ||
| #' \item{sd$log.ratios}{\code{GRanges} with all log.ratios.} | ||
| #' \item{sd$weights}{\code{GRanges} with interval weights.} | ||
| #' @author Markus Riester | ||
| #' | ||
| #' @export calculateIntervalWeights | ||
| calculateIntervalWeights <- function(normalDB, | ||
| interval.weight.file = NULL, top.quantile = 0.7, plot = FALSE, | ||
| normal.coverage.files = NULL) { | ||
| .Deprecated("createNormalDatabase") | ||
|
|
||
| # TODO, defunct in 1.18 | ||
| old_method <- FALSE | ||
| if (!is.null(normal.coverage.files) && missing(normalDB)) { | ||
| flog.warn("normal.coverage.files is deprecated, provide normalDB instead.") | ||
| old_method = TRUE | ||
| } else if (class(normalDB) == "character" && all(sapply(normalDB, file.exists))) { | ||
| flog.warn("Providing normal coverage files is deprecated. Provide a normalDB instead.") | ||
| normal.coverage.files <- normalDB | ||
| old_method = TRUE | ||
| } else { | ||
| normal.coverage.files <- normalDB[["normal.coverage.files"]] | ||
| } | ||
| flog.info("Loading coverage data...") | ||
| normal.coverage <- lapply(normal.coverage.files, readCoverageFile) | ||
| .calculateIntervalWeights(normalDB, normal.coverage, interval.weight.file, top.quantile, | ||
| plot, old_method) | ||
| calculateIntervalWeights <- function() { | ||
| .Defunct("createNormalDatabase") | ||
| } | ||
|
|
||
| .calculateIntervalWeights <- function(normalDB, normal.coverage, | ||
| interval.weight.file = NULL, top.quantile = 0.7, plot = FALSE, | ||
| old_method = FALSE) { | ||
|
|
||
| tumor.coverage <- list(poolCoverage(normal.coverage, | ||
| w = rep(1, length(normal.coverage)) / length(normal.coverage))) | ||
|
|
||
| if (old_method) { | ||
| lrs <- lapply(tumor.coverage, function(tc) sapply(normal.coverage, | ||
| function(nc) calculateLogRatio(nc, tc))) | ||
| } else { | ||
| lrs <- lapply(normal.coverage, function(x) calculateTangentNormal(x, normalDB)$log.ratio) | ||
| } | ||
|
|
||
| lrs <- do.call(cbind, lrs) | ||
|
|
||
| lrs[is.infinite(lrs)] <- NA | ||
|
|
||
| intervals <- normal.coverage[[1]] | ||
| mcols(intervals) <- NULL | ||
|
|
||
| lrs.sd <- apply(lrs, 1, sd, na.rm = TRUE) | ||
| lrs.cnt.na <- apply(lrs, 1, function(x) sum(is.na(x))) | ||
| # get the top.quantile % of sd by chromosome and use this to normalize weight=1 | ||
| chrom <- as.character(seqnames(intervals)) | ||
| sdCutoffByChr <- sapply(split(lrs.sd, chrom), quantile, probs = top.quantile, | ||
| names = FALSE, na.rm = TRUE)[chrom] | ||
|
|
||
| zz <- sdCutoffByChr / lrs.sd | ||
| zz[zz > 1] <- 1 | ||
| idx <- is.na(zz) | lrs.cnt.na > ncol(lrs) / 3 | ||
| zz[idx] <- min(zz, na.rm = TRUE) | ||
|
|
||
| ret <- list( | ||
| log.ratios = GRanges(intervals,,, DataFrame(lrs)), | ||
| weights = GRanges(intervals,,, DataFrame(weights = zz))) | ||
|
|
||
| if (!is.null(interval.weight.file)) { | ||
| ret_output <- data.frame( | ||
| Target = as.character(ret$weights), | ||
| weights = ret$weights$weights) | ||
|
|
||
| fwrite(ret_output, file = interval.weight.file, row.names = FALSE, | ||
| quote = FALSE, sep = "\t") | ||
| } | ||
| if (plot) .plotIntervalWeights(lrs.sd, width(tumor.coverage[[1]]), | ||
| tumor.coverage[[1]]$on.target) | ||
| if (old_method) return(NULL) | ||
| normalDB$sd <- ret | ||
| normalDB | ||
| } | ||
|
|
||
| #' Calculate target weights | ||
| #' | ||
| #' This function is defunct, use \code{\link{calculateIntervalWeights}} | ||
| #' instead. | ||
| #' | ||
| #' @author Markus Riester | ||
| #' | ||
| #' @export createTargetWeights | ||
| createTargetWeights <- function() { | ||
| .Defunct("calculateIntervalWeights") | ||
| } | ||
|
|
||
| .plotIntervalWeights <- function(lrs.sd, width, on.target) { | ||
| par(mfrow = c(1, 2)) | ||
| plot(width[on.target], lrs.sd[on.target], ylim = c(0,2), | ||
| xlab = "Interval Width", ylab = "log2 ratio sd.", main = "On-Target") | ||
| if (sum(!on.target)) { | ||
| plot(width[!on.target], lrs.sd[!on.target], col = "red", | ||
| ylim = c(0, 2), xlab = "Interval Width", ylab = "log2 ratio sd.", | ||
| main = "Off-Target") | ||
| } | ||
| } |
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