From 9d28f8c6620873ca11e5452f5a1c7fbf9e537296 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Jan 2026 14:30:33 -0500 Subject: [PATCH 1/3] update infercnv_success -> infercnv_status and modify description --- docs/merged_objects.md | 2 +- docs/sce_file_contents.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/merged_objects.md b/docs/merged_objects.md index 35499ed..14924e4 100644 --- a/docs/merged_objects.md +++ b/docs/merged_objects.md @@ -195,7 +195,7 @@ Each such list will contain the following fields: | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will not be present | | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will be `NA` | | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | -| `infercnv_success` | Boolean indicating if `inferCNV` succeeded. `TRUE` indicates that `inferCNV` successfully ran, `FALSE` indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and `NA` indicates that `inferCNV` was not run due to insufficient normal reference cells. Only present when CNV inference was attempted | +| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | | `infercnv_options` | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed | | `infercnv_table` | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed | diff --git a/docs/sce_file_contents.md b/docs/sce_file_contents.md index 08b5a0a..3985864 100644 --- a/docs/sce_file_contents.md +++ b/docs/sce_file_contents.md @@ -190,7 +190,7 @@ metadata(sce) # experiment metadata | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will not be present | | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will be `NA` | | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | -| `infercnv_success` | Boolean indicating if `inferCNV` succeeded. `TRUE` indicates that `inferCNV` successfully ran, `FALSE` indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and `NA` indicates that `inferCNV` was not run due to insufficient normal reference cells. Only present when CNV inference was attempted | +| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | | `infercnv_options` | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed | | `infercnv_table` | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed | From 9608e99c7197d0dfb3f3cdd387f5b6ac3b0fb86c Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Jan 2026 14:32:41 -0500 Subject: [PATCH 2/3] also mention non-cancerous --- docs/merged_objects.md | 2 +- docs/sce_file_contents.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/merged_objects.md b/docs/merged_objects.md index 14924e4..d43fd7b 100644 --- a/docs/merged_objects.md +++ b/docs/merged_objects.md @@ -195,7 +195,7 @@ Each such list will contain the following fields: | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will not be present | | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will be `NA` | | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | -| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | +| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | | `infercnv_options` | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed | | `infercnv_table` | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed | diff --git a/docs/sce_file_contents.md b/docs/sce_file_contents.md index 3985864..ecfd848 100644 --- a/docs/sce_file_contents.md +++ b/docs/sce_file_contents.md @@ -190,7 +190,7 @@ metadata(sce) # experiment metadata | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will not be present | | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will be `NA` | | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | -| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, and "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | +| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | | `infercnv_options` | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed | | `infercnv_table` | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed | From fc3be52635075714cb948cdceb922f49d91db388 Mon Sep 17 00:00:00 2001 From: "Stephanie J. Spielman" Date: Wed, 28 Jan 2026 15:01:21 -0500 Subject: [PATCH 3/3] Apply suggestions from code review - too many indicates Co-authored-by: Ally Hawkins <54039191+allyhawkins@users.noreply.github.com> --- docs/merged_objects.md | 2 +- docs/sce_file_contents.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/merged_objects.md b/docs/merged_objects.md index d43fd7b..1f02e3c 100644 --- a/docs/merged_objects.md +++ b/docs/merged_objects.md @@ -195,7 +195,7 @@ Each such list will contain the following fields: | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will not be present | | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample was obtained from normal or non-cancerous tissue this will be `NA` | | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | -| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | +| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | | `infercnv_options` | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed | | `infercnv_table` | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed | diff --git a/docs/sce_file_contents.md b/docs/sce_file_contents.md index ecfd848..a049fe3 100644 --- a/docs/sce_file_contents.md +++ b/docs/sce_file_contents.md @@ -190,7 +190,7 @@ metadata(sce) # experiment metadata | `infercnv_reference_celltypes` | Vector of consensus cell type labels which would be specified for the normal reference cells in `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will not be present | | `infercnv_num_reference_cells` | The total number of normal reference cells included in the `inferCNV` reference. Only present when consensus cell types were assigned and CNV inference was attempted. If CNV inference was attempted and the sample is obtained from normal or non-cancerous tissue this will be `NA` | | `infercnv_diagnosis_groups` | The broad diagnosis group used to determine which cell types should be considered as part of the normal cell reference for `inferCNV`. If this value is `Non-cancerous`, `inferCNV` was not run | -| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | +| `infercnv_status` | String indicating the status of running `inferCNV`. A value of "success" indicates that `inferCNV` successfully ran, "failure" indicates that `inferCNV` was attempted but failed during inference for an unknown reason, "insufficient_reference_cells" indicates that `inferCNV` was not run due to insufficient normal reference cells, and "skipped_non_cancerous" indicates that `inferCNV` was not run because the sample was non-cancerous. Other string values may be present if different errors running `inferCNV` were encountered, the specific details for which are provided in the QC report. Only present when CNV inference was attempted | | `infercnv_options` | A list containing the contents of the `objects` slot from the [final `inferCNV` results object](https://github.com/broadinstitute/infercnv/wiki/Output-Files#infercnv-object-files) containing all parameters specified used when running `inferCNV`. Only present when CNV inference was performed | | `infercnv_table` | The `inferCNV` metadata table with detailed CNV results output from `inferCNV`. This data frame corresponds to the [`map_metadata_from_infercnv.txt` table calculated from the HMM results](https://github.com/broadinstitute/infercnv/wiki/Extracting-features). Only present when CNV inference was performed |