From 0bc832e8161be02efb8f3b604607495e18f01e68 Mon Sep 17 00:00:00 2001 From: Ally Hawkins Date: Thu, 25 Jul 2024 15:28:11 -0500 Subject: [PATCH] age timing is always diagnosis when sample was collected at diagnosis --- docs/download_files.md | 2 +- docs/merged_objects.md | 2 +- docs/sce_file_contents.md | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/download_files.md b/docs/download_files.md index a1ef7b5..b69486d 100644 --- a/docs/download_files.md +++ b/docs/download_files.md @@ -104,7 +104,7 @@ Each row corresponds to a unique sample/library combination and contains the fol | `subdiagnosis` | Subcategory of diagnosis or mutation status (if applicable) | | `disease_timing` | At what stage of disease the sample was obtained, either diagnosis or recurrence | | `age` | Age provided by submitter | -| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`| +| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`. This will be `diagnosis` for all samples collected at diagnosis, indicated by the `disease_timing` column | | `sex` | Sex of patient that the sample was obtained from | | `tissue_location` | Where in the body the tumor sample was located | | `participant_id` | Unique id corresponding to the donor from which the sample was obtained | diff --git a/docs/merged_objects.md b/docs/merged_objects.md index 4c04b52..8ad29a7 100644 --- a/docs/merged_objects.md +++ b/docs/merged_objects.md @@ -198,7 +198,7 @@ metadata(merged_sce)$sample_metadata # sample metadata only for projects with mu | `submitter_id` | Original sample identifier from submitter | | `submitter` | Submitter name/ID | | `age` | Age provided by submitter | -| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`| +| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`. This will be `diagnosis` for all samples collected at diagnosis, indicated by the `disease_timing` column | | `sex` | Sex of patient that the sample was obtained from | | `diagnosis` | Tumor type | | `subdiagnosis` | Subcategory of diagnosis or mutation status (if applicable) | diff --git a/docs/sce_file_contents.md b/docs/sce_file_contents.md index 80b9b9f..a2d5389 100644 --- a/docs/sce_file_contents.md +++ b/docs/sce_file_contents.md @@ -176,7 +176,7 @@ The following columns are included in the sample metadata data frame for all lib | `submitter_id` | Original sample identifier from submitter | | `submitter` | Submitter name/ID | | `age` | Age provided by submitter | -| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`| +| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`. This will be `diagnosis` for all samples collected at diagnosis, indicated by the `disease_timing` column | | `sex` | Sex of patient that the sample was obtained from | | `diagnosis` | Tumor type | | `subdiagnosis` | Subcategory of diagnosis or mutation status (if applicable) | @@ -391,7 +391,7 @@ The `AnnData` object also includes the following additional cell-level metadata | `submitter_id` | Original sample identifier from submitter | | `submitter` | Submitter name/ID | | `age` | Age provided by submitter | -| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`| +| `age_timing` | Whether age is the age at diagnosis (`diagnosis`), age at collection (`collection`), or `unknown`. This will be `diagnosis` for all samples collected at diagnosis, indicated by the `disease_timing` column | | `sex` | Sex of patient that the sample was obtained from | | `diagnosis` | Tumor type | | `subdiagnosis` | Subcategory of diagnosis or mutation status (if applicable) |