create_core_matrix: Core matrix is a merge between gencode, entrez and hgnc data.

In svenstringer/genematrix: Create a Table with Gene Annotation and Output in Convenient Format

Description

Gene definitions are based on gencode. Entrez ids and official hgnc symbols are merged in Gene symbols in the resulting file are unique and only contains gencode genes that could be reliably matched with entrez and hgnc data. All three data sources are preprocessed and filtered before matching (see repsective preprocessing and merge functions for details).

Usage

create_core_matrix(gencode_url, hgnc_url, entrez_url, value_sep, download_dir)

Arguments

gencode_url	url to download gencode file from.
hgnc_url	url to download hgnc file from.
entrez_url	url to download entrez file from.
value_sep	character string separating values in multi-value fields.
download_dir	directory to save gencode, hgnc, and entrez source files.

Value

a data.table with core gene matrix

svenstringer/genematrix documentation built on May 30, 2019, 8:48 p.m.