umccrise_outputs: Get umccrise final output files

In pdiakumis/woofr: Helper R Functions for woof

Get umccrise final output files

Description

Generates a tibble containing absolute paths to umccrise final files.

Usage

umccrise_outputs(d)

Arguments

d	Path to ⁠<umccrised/sampleid__tumorid>⁠ umccrise directory.

Value

A tibble with the following columns:

• ftype: file type. Can be one of:

  • snv (single-nucleotide/indel variants VCF)

  • sv (Manta structural variants VCF)

  • cnv (PURPLE copy number variants)

  • multiqc (MultiQC JSON)

  • hrd (HRDetect or CHORD TSV results)

  • canrep_qcsum (QC summary from Cancer Report Rmd)

• flabel: file label (e.g. multiqc, sage, purple etc.)

• fpath: path to file

Examples

## Not run: 
um <- "path/to/umccrised/sample"
umccrise_outputs(um)

## End(Not run)

pdiakumis/woofr documentation built on Jan. 4, 2024, 11:22 a.m.