Merge pull request #336 from AlexsLemonade/allyhawkins/diagnosis-age-…

…timing-clarification Update age timing description to note that it is always diagnosis at diagnosis
AlexsLemonade · Jul 25, 2024 · 391982b · 391982b
2 parents b890694 + 0bc832e
commit 391982b
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 4 deletions.
diff --git 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
@@ -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
@@ -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)                                                                                                                                                                               |