Argos-Report

Version v1.0.3 (BALTO)

Scripts to load data from Argos output folders and process into tables to facilitate the creation of RMarkdown reports.

Usage:

In your R or RMarkdown source the load_data.R file and call the load_data function. Example:

# params gets passed by `rmarkdown::render`
#
source("load_data.R")
inputs=params
data=load_data(params$sample_id,params$inputs)

Inputs

• sample_id is one of the samples from that run. No checking is done so a fatal error will occur if the sample_id is not in the following inputs folders. (FIX THIS)

• inputs is a list with two (3) elements:

  • analysis_dir = the path to the ARGOS/HELIX analysis directory. It is the folder that contains the .muts.maf$ file.
  • portal_dir = the path to the ARGOS/HELIX portal directory. It folder that contains the data_clinical_sample.txt file.
  • oncokb_file = path to the oncokb annotation file

Outputs

The return value is a list with the following elements:

• tbl01 - Sample metadata (id's, type, matched normal, ...)
• summaryTbl - Summary of alterations
• mafTbl - Mutation Table. Will be filtered with ExAC-filter if unmatched
• mafTblFull - Unfiltered Mutation Table for case of unmatched normal (same as mafTbl for matched case)
• cnvTbl - Filtered Copy Number Table, DMP convention of only HOMODEL & AMP
• cnvTblFull - Full Copy Number Table
• fusionTbl - Fusion Events
• reportTbl - Report info (version, input directory)
• methods - Methods paragraph
• glossaryTbl - Glossary table with various definitions