From 25d7d1434f2c4faf88764443556c247edeb577fa Mon Sep 17 00:00:00 2001 From: Ethan Bass Date: Mon, 11 Dec 2023 18:09:52 -0500 Subject: [PATCH] fix: get_peaktable new bug --- R/get_peaktable.R | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/R/get_peaktable.R b/R/get_peaktable.R index 7085c2b..0f389e8 100644 --- a/R/get_peaktable.R +++ b/R/get_peaktable.R @@ -150,10 +150,11 @@ get_peaktable <- function(peak_list, chrom_list, response = c("area", "height"), sing <- which(pkcenters.cl == 0) pkcenters.cl[sing] <- max(pkcenters.cl) + seq_along(sing) } - vars <- c(rt, "start", "end", "sd", "tau", "FWHM", "r.squared", "purity") + vars <- c(rt, "start", "end", "sd", "width", "tau", "FWHM", "r.squared", "purity") + vars <- vars[vars %in% colnames(xx)] vars.idx <- match(vars, colnames(xx)) cl.centers <- aggregate(xx[, vars.idx], by = list(pkcenters.cl), FUN = "mean", - na.action = "na.pass")[, -1] + na.action = "na.pass")[, -1, drop = FALSE] ncl <- length(cl.centers[, rt]) ## re-order clusters from small to large rt @@ -179,10 +180,11 @@ get_peaktable <- function(peak_list, chrom_list, response = c("area", "height"), panel.abline(v = cl.centers[,rt], col = mycols) })) } - if (verbose & max(clusCount <- table(file.idx, pkcenters.cl)) > 1) + if (verbose & max(clusCount <- table(file.idx, pkcenters.cl)) > 1){ warning(paste("More than one peak of one injection in the same cluster", paste("for component ", comp, ".", sep = ""), "Keeping only the most intense one.", "", sep = "\n")) + } allIs <- unlist(lapply(pkLst, function(samp) samp[[comp]][, response])) Iinfo <- matrix(0, ncl, length(pkLst), dimnames = list(NULL, names(pkLst))) for (i in seq(along = allIs)){