Package 'TPACData'

Title: Human Protein Atlas Data for Tissue-Adjusted Pathway Analysis of Cancer (TPAC)
Description: Contains summary data on gene expression in normal human tissues from the Human Protein Atlas for use with the Tissue-Adjusted Pathway Analysis of cancer (TPAC) method. Frost, H. Robert (2023) "Tissue-adjusted pathway analysis of cancer (TPAC)" <doi:10.1101/2022.03.17.484779>.
Authors: H. Robert Frost [aut, cre]
Maintainer: H. Robert Frost <[email protected]>
License: GPL (>= 2)
Version: 0.1.0
Built: 2024-12-17 06:30:14 UTC
Source: CRAN

Help Index

Gene expression data for normal human tissues from the Human Protein Atlas (HPA). This data was specially processed by the HPA group as FPKM values (file "HPA.normal.FPKM.GDCpipeline.csv") using a pipeline similar to that employed by GDC for the TCGA RNA-seq data.

Description

A data.table with 1,088,694 rows and 4 columns (Gene, Tissue, FPKM, TissueSpecificity):

  • Gene: Ensembl gene ID

  • Tissue: Human tissue type

  • FPKM: Mean expression of that gene in units FPKM+1

  • TissueSpecificity: The fold-change in expression between mean expression in that tissue and mean in all 18 tissues.

Usage

hpa.data

Format

A data.table with 1,088,694 rows and 4 columns (Gene, Tissue, FPKM, TissueSpecificity)

Source

Human Protein Atlas

References

  • Ulhen et al. (2017). A pathology atlas of the human cancer transcriptome. Science. doi: 10.1126/science.aan2507