deTS (version 1.0)

tsea.analysis: Tissue-specific enrichment analysis for query gene list

Description

Tissue-specific enrichment analysis by Fisher's Exact Test for given gene list.

Usage

tsea.analysis(query_gene_list, score, ratio = 0.05,
p.adjust.method = "BH")

Arguments

query_gene_list

a gene symbol list object.

score

a gene tissue-specific score matrix, c("GTEx_t_score" or "ENCODE_z_score"), can be loaded by data(GTEx) or data(ENCODE), the default value is recommended "GTEx_t_score".

ratio

the threshold to define tissue-specific genes (with top t-score or z-score), the default value is 0.05.

p.adjust.method

p.adjust.method, c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")

Value

A data frame with p-value of tissue-specific enrichment result.

Rows stand for tissue names and columns stand for sample names.

Details

Tissue-specific enrichment analysis by Fisher's Exact Test for given gene list.

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

# NOT RUN {
data(GWAS_gene)
data(GTEx_t_score)
query_gene_list = GWAS_gene
tsea_t = tsea.analysis(query_gene_list, GTEx_t_score, 0.05,
	p.adjust.method = "bonferroni")
# }