diff --git a/R/LFQDataStats.R b/R/LFQDataStats.R index 0253edb7..b0dc40bf 100644 --- a/R/LFQDataStats.R +++ b/R/LFQDataStats.R @@ -27,9 +27,9 @@ #' stopifnot(is.null(x$power_t_test_quantiles())) #' } #' } -#' istar <- prolfqua_data('data_ionstar')$filtered() -#' istar$config <- old2new(istar$config) -#' data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100)) +#' bb <- prolfqua::sim_lfq_data_peptide_config() +#' istar$config <- bb$config +#' data <-bb$data #' lfqdata <- LFQData$new(data, istar$config) #' lfqstats <- lfqdata$get_Stats() #' lfqstats$stats_wide() @@ -39,10 +39,7 @@ #' #' #study variance of normalized data #' -#' istar <- prolfqua_data('data_ionstar')$normalized() -#' istar$config <- old2new(istar$config) -#' istar$config$table$is_response_transformed -#' data <- istar$data |> dplyr::filter(protein_Id %in% sample(protein_Id, 100)) +#' #' lfqdata <- LFQData$new(data, istar$config) #' lfqdata$is_transformed(TRUE) #' lfqstats <- lfqdata$get_Stats() @@ -50,13 +47,6 @@ #' #' #Slightly different dataset #' -#' bb <- prolfqua_data('data_ionstar')$filtered() -#' bb$config <- old2new(bb$config) -#' stopifnot(nrow(bb$data) == 25780) -#' config <- bb$config$clone(deep = TRUE) -#' analysis <- bb$data -#' -#' lfqdata <- LFQData$new(analysis, config) #' #' # estimates statistics for all samples #' lfqstats <- lfqdata$get_Stats(stats = "all") @@ -110,7 +100,7 @@ LFQDataStats <- R6::R6Class( res <- tidyr::pivot_wider( self$statsdf,id_cols = self$lfq$config$table$hierarchy_keys() , names_from = self$lfq$config$table$factor_keys_depth(), - values_from = tidyselect::any_of( c("n", "not_na", "sd", "var", "mean", "CV"))) + values_from = tidyselect::any_of( c("nrReplicates", "nrMeasured", "sd", "var", "meanAbundance","medianAbundance", "CV"))) return(res) }, #' @description diff --git a/R/tidyMS_stats.R b/R/tidyMS_stats.R index 60537401..322ef77f 100644 --- a/R/tidyMS_stats.R +++ b/R/tidyMS_stats.R @@ -187,7 +187,7 @@ summarize_stats <- function(pdata, config, factor_key = config$table$factor_keys var = stats::var(!!intsym, na.rm = TRUE), meanAbundance = mean(!!intsym, na.rm = TRUE), medianAbundance = median(!!intsym, na.rm = TRUE), - .groups = "drop_last") |> dplyr::ungroup() + .groups = "drop") |> dplyr::ungroup() hierarchyFactor <- hierarchyFactor |> dplyr::mutate(dplyr::across(all_of(factor_key), as.character)) diff --git a/man/LFQDataStats.Rd b/man/LFQDataStats.Rd index d9a58f44..c08e324a 100644 --- a/man/LFQDataStats.Rd +++ b/man/LFQDataStats.Rd @@ -32,9 +32,9 @@ runallfuncs <- function(x){ stopifnot(is.null(x$power_t_test_quantiles())) } } -istar <- prolfqua_data('data_ionstar')$filtered() -istar$config <- old2new(istar$config) -data <- istar$data |> dplyr::filter(protein_Id \%in\% sample(protein_Id, 100)) +bb <- prolfqua::sim_lfq_data_peptide_config() +istar$config <- bb$config +data <-bb$data lfqdata <- LFQData$new(data, istar$config) lfqstats <- lfqdata$get_Stats() lfqstats$stats_wide() @@ -44,10 +44,7 @@ x <- lfqstats #study variance of normalized data -istar <- prolfqua_data('data_ionstar')$normalized() -istar$config <- old2new(istar$config) -istar$config$table$is_response_transformed -data <- istar$data |> dplyr::filter(protein_Id \%in\% sample(protein_Id, 100)) + lfqdata <- LFQData$new(data, istar$config) lfqdata$is_transformed(TRUE) lfqstats <- lfqdata$get_Stats() @@ -55,13 +52,6 @@ runallfuncs(lfqstats) #Slightly different dataset -bb <- prolfqua_data('data_ionstar')$filtered() -bb$config <- old2new(bb$config) -stopifnot(nrow(bb$data) == 25780) -config <- bb$config$clone(deep = TRUE) -analysis <- bb$data - -lfqdata <- LFQData$new(analysis, config) # estimates statistics for all samples lfqstats <- lfqdata$get_Stats(stats = "all")