diff --git a/DESCRIPTION b/DESCRIPTION index 25dc6b43..514585c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,8 +2,8 @@ Type: Package Package: gDRcore Title: Processing functions and interface to process and analyze drug dose-response data -Version: 1.3.9 -Date: 2024-08-09 +Version: 1.3.10 +Date: 2024-08-19 Authors@R: c( person("Bartosz", "Czech", , "bartosz.czech@contractors.roche.com", role = "aut", comment = c(ORCID = "0000-0002-9908-3007")), @@ -29,7 +29,7 @@ Imports: BiocParallel, checkmate, futile.logger, - gDRutils (>= 1.1.14), + gDRutils (>= 1.3.9), MultiAssayExperiment, purrr, stringr, diff --git a/NEWS.md b/NEWS.md index 48f976a1..9c8ed719 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +## gDRcore 1.3.10 - 2024-08-19 +* utilize `calc_sd` function + ## gDRcore 1.3.9 - 2024-08-09 * fix issue with wrong mapping of Day0 data diff --git a/R/average_SE.R b/R/average_SE.R index 9f407d3d..6e2bd4b3 100755 --- a/R/average_SE.R +++ b/R/average_SE.R @@ -92,7 +92,7 @@ average_FUN <- function(x, unmasked <- x[!masked, , drop = FALSE] agg_df <- unmasked[, list(mean(x, na.rm = TRUE), # set sd = 1 for single values - ifelse(length(x) == 1, 0, sd(x, na.rm = TRUE))), + gDRutils::calc_sd(x)), by = c("normalization_type", series_identifiers)] data.table::setorderv(agg_df, c(series_identifiers, "normalization_type")) data.table::setnames(agg_df, c("V1", "V2"), c("x", "x_std")) diff --git a/rplatform/dependencies.yaml b/rplatform/dependencies.yaml index a09aa4e3..e57789f1 100644 --- a/rplatform/dependencies.yaml +++ b/rplatform/dependencies.yaml @@ -1,6 +1,6 @@ pkgs: gDRutils: - ver: '>= 1.1.14' + ver: '>= 1.3.9' url: gdrplatform/gDRutils ref: main subdir: ~