Merge branch 'master' into vcf2

Boehringer-Ingelheim · Mar 7, 2024 · 6c55cf7 · 6c55cf7
2 parents 9aa2a50 + 980e27b
commit 6c55cf7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,7 @@ Authors@R:
 Description: This package provides convenience functions for reading real-world evidence data provided by Personalis into Bioconductor MultiAssayExperiment objects.
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 Depends:
     SummarizedExperiment,
     readxl,

diff --git a/R/personalis.R b/R/personalis.R
@@ -483,12 +483,6 @@ read_personalis_cnv_reports <- function(sample_paths) {
   all_cnv <- bind_rows(map(cnv_list, "cnv_report"))
   row_data <- all_cnv |>
     select(cnv_id, `Gene Symbol`, `Chromosome`, `Segment Start`, `Segment End`) |>
-  col_data <- bind_rows(map(cnv_list, "summary_stats")) |>
-    tibble::column_to_rownames("sample")
-
-  all_cnv <- bind_rows(map(cnv_list, "cnv_report"))
-  row_data <- all_cnv |>
-    select(cnv_id, `Gene Symbol`, `Sequence`, `Segment Start`, `Segment End`) |>
     distinct()
   stopifnot("cnv_id is not a unique identifier" = !any(duplicated(row_data$cnv_id)))