Description Usage Arguments Details Value Note Author(s) References See Also Examples
Tissue-specific enrichment analysis by Fisher's Exact Test for multiple gene list.
1 2 | tsea.analysis.multiple(query_gene_list, score, ratio = 0.05,
p.adjust.method = "BH")
|
query_gene_list |
a 0~1 gene~sample table object, row should be gene symbol, column should be sample name. In the table, gene labeled with 1 indicated it is target gene for a given sample, while 0 indicated it is not target in a given sample. |
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") |
Tissue-specific enrichment analysis by Fisher's Exact Test for multiple gene list.
A data frame with p-value of tissue-specific enrichment result.
Rows stand for tissue names and columns stand for sample names.
nothing
Guangsheng Pei
Pei G., Dai Y., Zhao Z. Jia P. (2019) deTS: Tissue-Specific Enrichment Analysis to decode tissue specificity. Bioinformatics, In submission.
https://github.com/bsml320/deTS
1 2 3 4 5 | data(GWAS_gene_multiple)
data(GTEx_t_score)
query_gene_list = GWAS_gene_multiple
tsea_t_multi = tsea.analysis.multiple(query_gene_list,
GTEx_t_score, 0.05, p.adjust.method = "BH")
|
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