From 1ca778f2b95d1687d56ccb515858abbf4f74a67e Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Wed, 26 Jun 2024 20:08:38 +1000 Subject: [PATCH] vignettes: fix typos --- vignettes/installation.Rmd | 2 +- vignettes/output.Rmd | 75 +++++++++++++++++++------------------- vignettes/running.Rmd | 2 +- 3 files changed, 39 insertions(+), 40 deletions(-) diff --git a/vignettes/installation.Rmd b/vignettes/installation.Rmd index f6ab1ed..97f31c7 100644 --- a/vignettes/installation.Rmd +++ b/vignettes/installation.Rmd @@ -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 diff --git a/vignettes/output.Rmd b/vignettes/output.Rmd index 5a2ab36..94eb7e8 100644 --- a/vignettes/output.Rmd +++ b/vignettes/output.Rmd @@ -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`) | @@ -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 |
diff --git a/vignettes/running.Rmd b/vignettes/running.Rmd index 6354095..c9b2e88 100644 --- a/vignettes/running.Rmd +++ b/vignettes/running.Rmd @@ -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: