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vignettes: fix typos
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@pdiakumis @sigven
pdiakumis authored and sigven committed Jun 26, 2024
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2 changes: 1 addition & 1 deletion vignettes/installation.Rmd
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Expand Up @@ -6,7 +6,7 @@ output: rmarkdown::html_document
CPSR is distributed alongside the [Personal Cancer Genome Reporter (PCGR)](https://github.com/sigven/pcgr), so please follow
the [PCGR installation steps](https://sigven.github.io/pcgr/articles/installation.html) to install CPSR, either through [Docker](https://docs.docker.com/), [Apptainer/Singularity](https://apptainer.org/docs/user/latest/index.html), or [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html).

We recommend [Conda](https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html) as the simplest framework to install PCGR and CPSR, using either a MacOS or a Linux platform.
We recommend Conda as the simplest framework to install PCGR and CPSR, using either a MacOS or a Linux platform.

Assuming you have installed the `pcgr` and `pcgrr` conda envs as described in the above links
at e.g. `/home/user/projects/cpsr_proj1/conda/env/`, you can load the `pcgr` environment and check
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75 changes: 37 additions & 38 deletions vignettes/output.Rmd
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Expand Up @@ -71,8 +71,7 @@ A VCF file containing annotated, germline calls (single nucleotide variants and
| `Feature_type` | Type of feature. Currently one of `Transcript`, `RegulatoryFeature`, `MotifFeature` (picked by VEP's `--flag_pick_allele` option) |
| `Feature` | Ensembl stable ID of feature (picked by VEP's `--flag_pick_allele` option) |
| `cDNA_position` | Relative position of base pair in cDNA sequence (picked by VEP's `--flag_pick_allele` option) |
| `CDS_position` | Relative position of base pair in coding
sequence (picked by VEP's `--flag_pick_allele` option) |
| `CDS_position` | Relative position of base pair in coding sequence (picked by VEP's `--flag_pick_allele` option) |
| `CDS_RELATIVE_POSITION` | Ratio of variant coding position to length of coding sequence |
| `CDS_CHANGE` | Coding, transcript-specific sequence annotation (picked by VEP's `--flag_pick_allele` option) |
| `AMINO_ACID_START` | Protein position indicating absolute start of amino acid altered (fetched from `Protein_position`) |
Expand Down Expand Up @@ -218,42 +217,42 @@ sequence (picked by VEP's `--flag_pick_allele` option) |
| `gnomADe_NFE_AF` | Non-Finnish European germline allele frequency ([gnomAD release 2.1](http://gnomad.broadinstitute.org/)) |
| `gnomADe_OTH_AF` | Other germline allele frequency ([gnomAD release 2.1](http://gnomad.broadinstitute.org/)) |
| `gnomADe_ASJ_AF` | Ashkenazi Jewish allele frequency ([gnomAD release 2.1](http://gnomad.broadinstitute.org/)) |
| `gnomaADe_non_cancer_ASJ_AF` | Alternate allele frequency for samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_EAS_AF` | Alternate allele frequency for samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AFR_AF` | Alternate allele frequency for samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AMR_AF` | Alternate allele frequency for samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_OTH_AF` | Alternate allele frequency for samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_NFE_AF` | Alternate allele frequency for samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_FIN_AF` | Alternate allele frequency for samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_SAS_AF` | Alternate allele frequency for samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AF` | Alternate allele frequency in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_ASJ_AC` | Alternate allele count for samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_EAS_AC` | Alternate allele count for samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AFR_AC` | Alternate allele count for samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AMR_AC` | Alternate allele count for samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_OTH_AC` | Alternate allele count for samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_NFE_AC` | Alternate allele frequency for samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_FIN_AC` | Alternate allele count for samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_SAS_AC` | Alternate allele count for samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AC` | Alternate allele count in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_ASJ_AN` | Total number of alleles in samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_EAS_AN` | Total number of alleles in samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AFR_AN` | Total number of alleles in samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AMR_AN` | Total number of alleles in samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_OTH_AN` | Total number of alleles in samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_NFE_AN` | Total number of alleles in samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_FIN_AN` | Total number of alleles in samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_SAS_AN` | Total number of alleles in samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AN` | Total number of alleles in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_ASJ_NHOMALT` | Count of homozygous individuals in samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_EAS_NHOMALT` | Count of homozygous individuals in samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AFR_NHOMALT` | Count of homozygous individuals in samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_AMR_NHOMALT` | Count of homozygous individuals in samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_OTH_NHOMALT` | Count of homozygous individuals in samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_NFE_NHOMALT` | Count of homozygous individuals in samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_FIN_NHOMALT` | Count of homozygous individuals in samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_SAS_NHOMALT` | Count of homozygous individuals in samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomaADe_non_cancer_NHOMALT` | Count of homozygous individuals in samples in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_ASJ_AF` | Alternate allele frequency for samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_EAS_AF` | Alternate allele frequency for samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AFR_AF` | Alternate allele frequency for samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AMR_AF` | Alternate allele frequency for samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_OTH_AF` | Alternate allele frequency for samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_NFE_AF` | Alternate allele frequency for samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_FIN_AF` | Alternate allele frequency for samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_SAS_AF` | Alternate allele frequency for samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AF` | Alternate allele frequency in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_ASJ_AC` | Alternate allele count for samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_EAS_AC` | Alternate allele count for samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AFR_AC` | Alternate allele count for samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AMR_AC` | Alternate allele count for samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_OTH_AC` | Alternate allele count for samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_NFE_AC` | Alternate allele frequency for samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_FIN_AC` | Alternate allele count for samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_SAS_AC` | Alternate allele count for samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AC` | Alternate allele count in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_ASJ_AN` | Total number of alleles in samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_EAS_AN` | Total number of alleles in samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AFR_AN` | Total number of alleles in samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AMR_AN` | Total number of alleles in samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_OTH_AN` | Total number of alleles in samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_NFE_AN` | Total number of alleles in samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_FIN_AN` | Total number of alleles in samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_SAS_AN` | Total number of alleles in samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AN` | Total number of alleles in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_ASJ_NHOMALT` | Count of homozygous individuals in samples of Ashkenazi Jewish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_EAS_NHOMALT` | Count of homozygous individuals in samples of East Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AFR_NHOMALT` | Count of homozygous individuals in samples of African-American/African ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_AMR_NHOMALT` | Count of homozygous individuals in samples of Latino ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_OTH_NHOMALT` | Count of homozygous individuals in samples of Other ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_NFE_NHOMALT` | Count of homozygous individuals in samples of Non-Finnish European ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_FIN_NHOMALT` | Count of homozygous individuals in samples of Finnish ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_SAS_NHOMALT` | Count of homozygous individuals in samples of South Asian ancestry in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `gnomADe_non_cancer_NHOMALT` | Count of homozygous individuals in samples in the non-cancer subset ([gnomAD 2.1.1](http://gnomad.broadinstitute.org)) |
| `DBSNP_RSID` | [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/) reference ID, as provided by VEP |

<br>
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2 changes: 1 addition & 1 deletion vignettes/running.Rmd
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Expand Up @@ -212,7 +212,7 @@ cpsr \
--force_overwrite
```

Note that the example command refers to the PCGR data bundle directory (*refdata_dir*), which contains the data bundle that are necessary for both *PCGR* and *CPSR*.
Note that the example command refers to the PCGR data bundle directory (*refdata_dir*), which contains the data necessary for both *PCGR* and *CPSR*.

This command will produce the following output files in the _output_ folder:

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