Pre-computed data objects

Source: R/data.R

Pre-computed data objects

BIOCARTA_PATHWAYS

PATHWAY2BC

PATHWAY2ENTREZ

PATHWAY2MSIGDB

BC2ENTREZ

Format

An object of class list of length 314.

An object of class data.frame with 4428 rows and 2 columns.

An object of class data.frame with 5196 rows and 2 columns.

An object of class data.frame with 292 rows and 2 columns.

An object of class data.frame with 1739 rows and 2 columns.

Value

  • BIOCARTA_PATHWAYS: A list of pathway objects. The pathway object is explained in get_pathway().

  • PATHWAY2BC: A two-column data frame of pathway IDs and BC IDs.

  • PATHWAY2ENTREZ: A two-column data frame of pathway IDs and gene Entrez IDs.

  • PATHWAY2MSIGDB: A two-column data frame of pathway IDs and MSigDB IDs.

  • BC2ENTREZ: A two-column data frame of BC IDs and gene EntreZ IDs.

The nodes in the original BioCarta pathways are proteins and some of them do not have one-to-one mapping to genes, such as protein families or complex. Here BC_ID is the primary ID of proteins/single nodes in BioCarta Pathways and this package provides mapping to gene EntreZ IDs.

Details

BIOCARTA_PATHWAYS, PATHWAY2BC, PATHWAY2ENTREZ and BC2ENTREZ are collected from web.archive.org (https://web.archive.org/web/20170122225118/https://cgap.nci.nih.gov/Pathways/BioCarta_Pathways). PATHWAY2MSIGDB is collected from MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/human/genesets.jsp?collection=CP:BIOCARTA). The script for generating these datasets can be found at:

system.file("script", "process.R", package = "BioCartaImage")