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Generates a UMCCR Cancer Report. It does so with the following steps:

  1. move the img_dir into 'tmp/img_dir'

  2. copy the rmd into 'tmp/cancer_report.Rmd'

  3. render the rmd inside 'tmp/'

  4. return the path to the output HTML

Usage

cancer_rmd(
  af_global,
  af_keygenes,
  batch_name,
  bcftools_stats,
  conda_list,
  dragen_hrd,
  img_dir,
  key_genes,
  oncokb_genes,
  virusbreakend_tsv,
  virusbreakend_vcf,
  purple_purity,
  purple_qc,
  purple_som_cnv_ann,
  purple_som_cnv,
  purple_som_gene_cnv,
  purple_som_snv_vcf,
  somatic_snv_vcf,
  somatic_snv_summary,
  somatic_sv_tsv,
  somatic_sv_vcf,
  result_outdir,
  tumor_name,
  out_file = NULL,
  quiet = FALSE
)

Arguments

af_global

Path to af_tumor.txt file.

af_keygenes

Path to af_tumor_keygenes.txt file.

batch_name

Name of batch sample.

bcftools_stats

Path to bcftools_stats.txt file.

conda_list

Path to conda_pkg_list.txt file.

dragen_hrd

Path to DRAGEN hrdscore.csv file.

img_dir

Path to directory containing PURPLE plots.

key_genes

Path to UMCCR cancer gene file.

oncokb_genes

Path to OncoKB database file.

virusbreakend_tsv

Path to VIRUSBreakend summary file.

virusbreakend_vcf

Path to VIRUSBreakend VCF file.

purple_purity

Path to purple.purity.tsv.

purple_qc

Path to purple.qc.

purple_som_cnv_ann

Path to annotated and prioritised purple.cnv.somatic.tsv.

purple_som_cnv

Path to purple.cnv.somatic.tsv.

purple_som_gene_cnv

Path to purple.cnv.gene.tsv.

purple_som_snv_vcf

Path to purple.somatic.vcf.gz.

somatic_snv_vcf

Path to somatic-PASS.vcf.gz SNV VCF.

somatic_snv_summary

Path to somatic_snv_summary.json JSON.

somatic_sv_tsv

Path to SV TSV file.

somatic_sv_vcf

Path to SV VCF file.

result_outdir

Path to directory to write tidy JSON/TSV results.

tumor_name

Name of tumor sample.

out_file

Path to output HTML file (needs '.html' suffix) (def: {tumor_name}_cancer_report.html).

quiet

Suppress log printing during rendering.

Value

Path to rendered HTML report.