diff --git a/pcgrr/R/mutational_signatures.R b/pcgrr/R/mutational_signatures.R index 1e5f982b..78476526 100644 --- a/pcgrr/R/mutational_signatures.R +++ b/pcgrr/R/mutational_signatures.R @@ -125,8 +125,7 @@ generate_report_data_signatures <- sample_names = settings$sample_id, type = "all", genome = ref_data$assembly$bsg, - predefined_dbs_mbs = T) - ) + predefined_dbs_mbs = T)) ) if(class(grl)[1] == "CompressedGRangesList"){ @@ -326,7 +325,8 @@ generate_report_data_signatures <- gof <- list() gof[['ci_lower']] <- ci_data_gof$conf.int[1] gof[['ci_upper']] <- ci_data_gof$conf.int[2] - gof[['estimate']] <- mean(bootstrap_data[['goodness_of_fit']]$cosine_sim) + gof[['estimate']] <- + mean(bootstrap_data[['goodness_of_fit']]$cosine_sim) contributions_per_signature <- sig_prop_data |> @@ -371,7 +371,7 @@ generate_report_data_signatures <- dplyr::arrange( dplyr::desc(.data$prop_group)) |> dplyr::mutate(group = dplyr::if_else( - .data$prop_group > 0.05, + .data$prop_group > 0.03, .data$group, "Other")) |> dplyr::group_by(.data$group) |> @@ -419,11 +419,11 @@ generate_report_data_signatures <- contributions_per_group <- as.data.frame( contributions_per_group |> tidyr::separate_rows( - .data$signature_id_group, sep = ", ") |> + "signature_id_group", sep = ", ") |> dplyr::anti_join(missing_signatures, by = c("signature_id_group" = "signature_id")) |> dplyr::group_by( - c("group","prop_group") + group, prop_group ) |> dplyr::summarise( signature_id_group = paste(