| Type: | Package |
| Title: | Human Protein Atlas Data for Tissue-Adjusted Pathway Analysis of Cancer (TPAC) |
| Version: | 0.1.0 |
| 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>. |
| Depends: | R (≥ 3.6.0) |
| Imports: | data.table |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| LazyData: | true |
| LazyDataCompression: | bzip2 |
| NeedsCompilation: | no |
| Packaged: | 2023-10-23 13:13:48 UTC; d37329b |
| Author: | H. Robert Frost [aut, cre] |
| Maintainer: | H. Robert Frost <rob.frost@dartmouth.edu> |
| Repository: | CRAN |
| Date/Publication: | 2023-10-24 20:20:08 UTC |
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.dataFormat
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