oncotable: oncotable

In mskilab/skitools: Various mskilab R utilties

oncotable

Description

Takes as input (keyed) "tumors" (aka pairs) table which a metadata table with specific columns pointing to paths corresponding to one or more of the following pipeline outputs:

$annotated_bcf Path to annotated.bcf file that is the primary output of SnpEff module from which TMB and basic mutation descriptions are extracted along with their basic categories (these will comprising the core of the oncoplot are computed)

$fusions Path to fusion.rds file that is the primary output of the Fusions modjle, from which protein coding fusions will be computed for

$jabba_rds Path to jabba.simple.rds output representing primary output of JaBbA module from which SCNA and overall junction burden are computed

$complex Path to complex.rds gGnome cached object that is the primary output of Events module, from which simple and complex event burdens are computed

$signature_counts Path to signature_counts.txt that is the primary output of Signatures module from which SNV signature counts are computed

The function then outputs a melted data.table of "interesting" features that can be saved and/or immediately output into oncoprint. This data.table will at the very least have fields $id $type (event type), $track, and $source populated in addition to a few other data type specific columns.

The $source column is the name of the column of tumors from which that data was extracted, and track is a grouping variable that allows separation of the various data types.

All the paths above can be NA or non existent, in which case a dummy row is inserted into the table so that downstream applications know that data is missing for that sample.

Usage

oncotable(
  tumors,
  gencode = "http://mskilab.com/fishHook/hg19/gencode.v19.genes.gtf",
  verbose = TRUE,
  amp.thresh = 4,
  filter = "PASS",
  del.thresh = 0.5,
  mc.cores = 1
)

Arguments

tumors	keyed data.table i.e. keyed by unique tumor id with specific columns corresponding to paths to pipeline outputs(see description)
gencode	path to gencode with just a single entry for each gene (so gencode entries for each gene are collapse to a single range). The input could be .gtf or .rds with GRanges object, or a GRanges object i.e. resulting from importing the (appropriate) GENCODE .gtf via rtracklayer, note: this input is only used in CNA to gene mapping. If nothing is provided then 'http://mskilab.com/fishHook/hg19/gencode.v19.genes.gtf' is used by default.
verbose	logical flag
amp.thresh	SCNA amplification threshold to call an amp as a function of ploidy (4)
del.thresh	SCNA deletion threshold for (het) del as a function of ploidy (by default cn = 1 will be called del, but this allows additoinal regions in high ploidy tumors to be considered het dels)
mc.cores	number of cores for multithreading

Author(s)

Marcin Imielinski

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.