| deTS-package {deTS} | R Documentation |
Tissue-Specific Enrichment Analysis Tissue-Specific Enrichment Analysis
Description
Tissue-specific enrichment analysis to assess lists of candidate genes and tissue-specific expression decode analysis for RNA-seq data to decode RNA expression matrices tissue heterogeneity.
Details
Since disease and physiological condition are often associated with a specific tissue, understanding the tissue-specific genes (TSG) expression patterns will substantially reduce false discoveries in biomedical research. However, due to cell complexity in human system, heterogeneous tissues are frequently collected. Making it difficult to distinguish gene expression variability and mislead result interpretation. Here, we present deTS, an R package that conducts Tissue-Specific Enrichment Analysis (TSEA) using two built-in reference panels: the Genotype-Tissue Expression (GTEx) data and the ENCyclopedia Of DNA Elements (ENCODE) data. We implemented two major functions in TSEA to assess lists of candidate genes or expression matrices.
The DESCRIPTION file:
| Package: | deTS |
| Type: | Package |
| Title: | Tissue-Specific Enrichment Analysis |
| Version: | 1.0 |
| Date: | 2019-02-06 |
| Author: | Guangsheng Pei |
| Maintainer: | Guangsheng Pei <peiguangsheng@gmail.com> |
| Imports: | pheatmap, RColorBrewer |
| Description: | Tissue-specific enrichment analysis to assess lists of candidate genes or RNA-Seq expression profiles. Pei G., Dai Y., Zhao Z. Jia P. (2019) deTS: Tissue-Specific Enrichment Analysis to decode tissue specificity. Bioinformatics, In submission. |
| License: | GPL (>= 2) |
Index of help topics:
ENCODE_z_score ENCODE z-score to define tissue-specific genes
GTEx_t_score GTEx t-score to define tissue-specific genes
GWAS_gene Gene symbol query data for single sample
GWAS_gene_multiple Gene symbol query data for multiple samples
correction_factor Gene average expression level and standard
deviation in GTEx data
deTS-package Tissue-Specific Enrichment Analysis
Tissue-Specific Enrichment Analysis
query_ENCODE ENCODE raw query data
query_GTEx GTEx raw query data
tsea.analysis Tissue-specific enrichment analysis for query
gene list
tsea.analysis.multiple
Tissue-specific enrichment analysis for multi
query gene lists
tsea.expression.decode
Tissue-specific enrichment analysis for RNA-Seq
expression profiles
tsea.expression.normalization
RNA-Seq expression profiles normalization
tsea.plot Tissue-specific enrichment analysis result
heatmap plot
tsea.summary Tissue-specific enrichment analysis result
summary
Author(s)
Guangsheng Pei
Maintainer: Guangsheng Pei
References
Pei G., Dai Y., Zhao Z., Jia P. (2019) deTS: Tissue-Specific Enrichment Analysis to decode tissue specificity. Bioinformatics, In submission.
See Also
https://github.com/bsml320/deTS
Examples
data(GTEx_t_score)
data(ENCODE_z_score)
library(pheatmap)
data(GWAS_gene)
query_gene_list = GWAS_gene
tsea_t = tsea.analysis(query_gene_list, GTEx_t_score, 0.05,
p.adjust.method = "bonferroni")
tsea_t_summary = tsea.summary(tsea_t)
data(GWAS_gene_multiple)
query_gene_list = GWAS_gene_multiple[,1:2]
tsea_t_multi = tsea.analysis.multiple(query_gene_list,
GTEx_t_score, 0.05, p.adjust.method = "BH")
data(query_GTEx)
query_matrix = query_GTEx[,1:2]
data(correction_factor)
query_mat_zscore_nor = tsea.expression.normalization(query_matrix,
correction_factor, normalization = "z-score")
tseaed_in_ENCODE = tsea.expression.decode(query_mat_zscore_nor,
ENCODE_z_score, 0.05, p.adjust.method = "BH")
tseaed_in_ENCODE_summary = tsea.summary(tseaed_in_ENCODE)