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Update analyses/README and module's README to reflect changes (#525)
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- update `README` files to reflect changes to the focal -cn-file-preparation module in PR #493

Co-authored-by: Jaclyn Taroni <jaclyn.n.taroni@gmail.com>
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@cbethell @jaclyn-taroni
cbethell and jaclyn-taroni authored Feb 7, 2020
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2 changes: 1 addition & 1 deletion analyses/README.md
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Expand Up @@ -18,7 +18,7 @@ Note that _nearly all_ modules use the harmonized clinical data file (`pbta-hist
| [`comparative-RNASeq-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/comparative-RNASeq-analysis) | `pbta-gene-expression-rsem-tpm.polya.rds` <br> `pbta-gene-expression-rsem-tpm.stranded.rds` | *In progress*; will produce expression outlier profiles per [#229](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/229) | N/A |
| [`copy_number_consensus_call`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/copy_number_consensus_call) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-sv-manta.tsv.gz` | Produces consensus copy number calls per [#128](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/128) and a set of excluded regions where CNV calls are not made | `results/cnv_consensus.tsv` <br> `results/pbta-cnv-consensus.seg.gz` <br> `ref/cnv_excluded_regions.bed` <br> `ref/cnv_callable.bed`
| [`create-subset-files`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/create-subset-files) | All files | This module contains the code to create the subset files used in continuous integration | All subset files for continuous integration
| [`focal-cn-file-preparation`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/focal-cn-file-preparation) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm.polya.rds` <br> `pbta-gene-expression-rsem-fpkm.stranded.rds` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz` | Maps from copy number variant caller segments to gene identifiers; will be updated to take into account changes that affect entire cytobands, chromosome arms ([#186](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/186))| `results/cnvkit_annotated_cn_autosomes.tsv.gz` <br> `results/cnvkit_annotated_cn_x_and_y.tsv.gz` <br> `results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `results/controlfreec_annotated_cn_x_and_y.tsv.gz` <br> `results/consensus_seg_annotated_cn_autosomes.tsv.gz` <br> `results/consensus_seg_annotated_cn_x_and_y.tsv.gz`
| [`focal-cn-file-preparation`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/focal-cn-file-preparation) | `pbta-cnv-cnvkit.seg.gz` <br> `pbta-cnv-controlfreec.tsv.gz` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `analyses/copy_number_consensus_call/results/pbta-cnv-consensus.seg.gz` | Maps from copy number variant caller segments to gene identifiers; will be updated to take into account changes that affect entire cytobands, chromosome arms ([#186](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/186))| `results/cnvkit_annotated_cn_autosomes.tsv.gz` <br> `results/cnvkit_annotated_cn_x_and_y.tsv.gz` <br> `results/controlfreec_annotated_cn_autosomes.tsv.gz` <br> `results/controlfreec_annotated_cn_x_and_y.tsv.gz` <br> `results/consensus_seg_annotated_cn_autosomes.tsv.gz` <br> `results/consensus_seg_annotated_cn_x_and_y.tsv.gz`
| [`fusion_filtering`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion_filtering) | `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Standardizes, filters, and prioritizes fusion calls | `results/pbta-fusion-putative-oncogenic.tsv` <br> `results/pbta-fusion-recurrent-fusion-byhistology.tsv` <br> `results/pbta-fusion-recurrent-fusion-bysample.tsv` (included in data download)
| [`fusion-summary`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/fusion-summary)| `pbta-histologies.tsv` <br> `pbta-fusion-putative-oncogenic.tsv` <br> `pbta-fusion-arriba.tsv.gz` <br> `pbta-fusion-starfusion.tsv.gz` | Generate summary tables from fusion files ([#398](https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/398)) | `results/fusion_summary_embryonal_foi.tsv` <br> `results/fusion_summary_ependymoma_foi.tsv`
| [`gene-set-enrichment-analysis`](https://github.com/AlexsLemonade/OpenPBTA-analysis/tree/master/analyses/gene-set-enrichment-analysis) | `pbta-gene-expression-rsem-fpkm-collapsed.stranded.rds` <br> `pbta-gene-expression-rsem-fpkm-collapsed.polya.rds` | *In progress*. Updated gene set enrichment analysis with appropriate RNA-seq expression data | `results/gsva_scores_stranded.tsv` <br> `results/gsva_scores_polya.tsv` <br> for stranded, polya expression data respectively
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66 changes: 64 additions & 2 deletions analyses/focal-cn-file-preparation/README.md
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Expand Up @@ -29,8 +29,9 @@ See the notebook for more information.
| biospecimen_id | status | copy_number | ploidy | ensembl | gene_symbol | cytoband |
|----------------|--------|-------------|--------|---------|-------------|---------|

* `rna-expression-validation.R` - This script examines RNA-seq expression levels (RSEM FPKM) of genes that are called as deletions.
It is not currently run via the shell script.
* `rna-expression-validation.R` - This script examines RNA-seq expression levels (RSEM FPKM) of genes that are called as deletions.
It produces loss/neutral and zero/neutral correlation plots, as well as stacked barplots displaying the distribution of ranges in expression across each of the calls (loss, neutral, zero).
_Note: The shell script's default behavior is to produce these plots using the annotated consensus SEG autosome and sex chromsome files found in this module's `results` directory and listed below._

### Output files for downstream consumption

Expand All @@ -43,3 +44,64 @@ results
├── controlfreec_annotated_cn_autosomes.tsv.gz
└── controlfreec_annotated_cn_x_and_y.tsv.gz
```

### Folder Structure

```
focal-cn-file-preparation
├── 01-add-ploidy-cnvkit.Rmd
├── 01-add-ploidy-cnvkit.nb.html
├── 02-add-ploidy-consensus.Rmd
├── 02-add-ploidy-consensus.nb.html
├── 03-prepare-cn-file.R
├── README.md
├── display-plots.md
├── plots
│   ├── cnvkit_annotated_cn_autosomes_polya_loss_cor_plot.png
│   ├── cnvkit_annotated_cn_autosomes_polya_stacked_plot.png
│   ├── cnvkit_annotated_cn_autosomes_polya_zero_cor_plot.png
│   ├── cnvkit_annotated_cn_autosomes_stranded_loss_cor_plot.png
│   ├── cnvkit_annotated_cn_autosomes_stranded_stacked_plot.png
│   ├── cnvkit_annotated_cn_autosomes_stranded_zero_cor_plot.png
│   ├── cnvkit_annotated_cn_x_and_y_polya_loss_cor_plot.png
│   ├── cnvkit_annotated_cn_x_and_y_polya_stacked_plot.png
│   ├── cnvkit_annotated_cn_x_and_y_polya_zero_cor_plot.png
│   ├── cnvkit_annotated_cn_x_and_y_stranded_loss_cor_plot.png
│   ├── cnvkit_annotated_cn_x_and_y_stranded_stacked_plot.png
│   ├── cnvkit_annotated_cn_x_and_y_stranded_zero_cor_plot.png
│   ├── consensus_seg_annotated_cn_autosomes_polya_loss_cor_plot.png
│   ├── consensus_seg_annotated_cn_autosomes_polya_stacked_plot.png
│   ├── consensus_seg_annotated_cn_autosomes_polya_zero_cor_plot.png
│   ├── consensus_seg_annotated_cn_autosomes_stranded_loss_cor_plot.png
│   ├── consensus_seg_annotated_cn_autosomes_stranded_stacked_plot.png
│   ├── consensus_seg_annotated_cn_autosomes_stranded_zero_cor_plot.png
│   ├── consensus_seg_annotated_cn_x_and_y_polya_loss_cor_plot.png
│   ├── consensus_seg_annotated_cn_x_and_y_polya_stacked_plot.png
│   ├── consensus_seg_annotated_cn_x_and_y_polya_zero_cor_plot.png
│   ├── consensus_seg_annotated_cn_x_and_y_stranded_loss_cor_plot.png
│   ├── consensus_seg_annotated_cn_x_and_y_stranded_stacked_plot.png
│   ├── consensus_seg_annotated_cn_x_and_y_stranded_zero_cor_plot.png
│   ├── controlfreec_annotated_cn_autosomes_polya_loss_cor_plot.png
│   ├── controlfreec_annotated_cn_autosomes_polya_stacked_plot.png
│   ├── controlfreec_annotated_cn_autosomes_polya_zero_cor_plot.png
│   ├── controlfreec_annotated_cn_autosomes_stranded_loss_cor_plot.png
│   ├── controlfreec_annotated_cn_autosomes_stranded_stacked_plot.png
│   ├── controlfreec_annotated_cn_autosomes_stranded_zero_cor_plot.png
│   ├── controlfreec_annotated_cn_x_and_y_polya_loss_cor_plot.png
│   ├── controlfreec_annotated_cn_x_and_y_polya_stacked_plot.png
│   ├── controlfreec_annotated_cn_x_and_y_polya_zero_cor_plot.png
│   ├── controlfreec_annotated_cn_x_and_y_stranded_loss_cor_plot.png
│   ├── controlfreec_annotated_cn_x_and_y_stranded_stacked_plot.png
│   └── controlfreec_annotated_cn_x_and_y_stranded_zero_cor_plot.png
├── results
│   ├── cnvkit_annotated_cn_autosomes.tsv.gz
│   ├── cnvkit_annotated_cn_x_and_y.tsv.gz
│   ├── consensus_seg_annotated_cn_autosomes.tsv.gz
│   ├── consensus_seg_annotated_cn_x_and_y.tsv.gz
│   ├── controlfreec_annotated_cn_autosomes.tsv.gz
│   └── controlfreec_annotated_cn_x_and_y.tsv.gz
├── rna-expression-validation.R
├── run-prepare-cn.sh
└── util
└── rna-expression-functions.R
```

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