GSEA_score: Compute the enrichment score (ES) from Gene Set Enrichment...
In lusystemsbio/NetAct: NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity
GSEA_score R Documentation
Compute the enrichment score (ES) from Gene Set Enrichment Analysis
Description
In this specific implementation, we modified two aspects:
(1) the stats_vector takes the absolute value of the t-statistics;
This ensures that the GSEA works for the case where part of genes are up-regulated and others are down-regulated.
(2) permutation of the gene symbols of the ranking vector, instead of gene expression values.
Usage
GSEA_score(gene_list, gene_set, stats_vector)
Arguments
gene_list
a vector of genes in the expression data
gene_set
a vector of genes in the gene set
stats_vector
a vector of DEG statistics for every gene in gene_list (rank_vector in the DEG results)
Absolute values of the t-statistics are required for the desired performance.
Value
ES: enrichment score
lusystemsbio/NetAct documentation built on Sept. 7, 2024, 8:34 p.m.
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| GSEA_score | R Documentation |
Compute the enrichment score (ES) from Gene Set Enrichment Analysis
Description
In this specific implementation, we modified two aspects: (1) the stats_vector takes the absolute value of the t-statistics; This ensures that the GSEA works for the case where part of genes are up-regulated and others are down-regulated. (2) permutation of the gene symbols of the ranking vector, instead of gene expression values.
Usage
GSEA_score(gene_list, gene_set, stats_vector)
Arguments
gene_list |
a vector of genes in the expression data |
gene_set |
a vector of genes in the gene set |
stats_vector |
a vector of DEG statistics for every gene in gene_list (rank_vector in the DEG results) Absolute values of the t-statistics are required for the desired performance. |
Value
ES: enrichment score
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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