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.

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)

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

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