maf_data_pool_add_rnaseq: Add RNAseq - maf_data_pool version

In CCICB/CRUX: Easily explore patterns of somatic variation in cancer using 'CRUX'

Add RNAseq – maf_data_pool version

Description

Add RNA data to a dataset_wrapper within a maf_data_pool.

Usage

maf_data_pool_add_rnaseq(maf_data_pool, unique_name, rnaseq_path)

Arguments

maf_data_pool	see ?new_maf_data_pool for details (maf_data_pool)
unique_name	Unique name of the maf_data_wrapper. see ?new_maf_data_wrapper for details (string)
rnaseq_path	Path to rnaseq file (string)

Details

How this works: We read in the file at rnaseq_path as data frame, check if it looks like we expect. If so, the filepath is saved to the maf_dataset_wrapper (NOT THE DATAFRAME!). This is so we don't have to keep the RNA data in memory. When we go to export or visualise, we'll just reload it using maf_data_wrapper_get_rnaseq_df, which returns a dataframe (or NULL if none is found).

Also note that no cohort subsetting will affect this RNA file, as all we have is the filepath. This is not a problem, since the functions that export / visualise the data simply load it into memory, then check the clinical datafile to see which samples we need to export. If they've been subset out of the clinical datafile, the user probably wont want to export RNA data from these samples ... my export function are aware of this.

Also note, that this file wont be subset

Value

maf_data_pool with updated maf_data_pool_add_rnaseq

CCICB/CRUX documentation built on Jan. 28, 2024, 10:12 p.m.