pathway_genes: Genes in pathway
In diogocamacho/rpegeos: Pathway enrichment for gene expression signatures
Description
Usage
Arguments
Value
Description
Returns the number of genes in the query set that are present in a given pathway.
Usage
1
pathway_genes(gene_set, pathway_tfidf, fthr, pthr)
Arguments
gene_set
Query gene set of interest. Should be a Nx3 matrix, where column 1 is Entrez ID, column 2 is fold-change, and column 3 is p-value (recommend using FDR corrected p-values from a package like 'limma' or 'DESeq2')
pathway_tfidf
tf-idf matrix computed with tfidf
fthr
Fold change threshold
pthr
p-value threshold
Value
Returns vector with number of genes matched to any given pathway.
diogocamacho/rpegeos documentation built on June 4, 2019, 6:37 p.m.
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Description Usage Arguments Value
Description
Returns the number of genes in the query set that are present in a given pathway.
Usage
1 | pathway_genes(gene_set, pathway_tfidf, fthr, pthr)
|
Arguments
gene_set |
Query gene set of interest. Should be a Nx3 matrix, where column 1 is Entrez ID, column 2 is fold-change, and column 3 is p-value (recommend using FDR corrected p-values from a package like 'limma' or 'DESeq2') |
pathway_tfidf |
tf-idf matrix computed with |
fthr |
Fold change threshold |
pthr |
p-value threshold |
Value
Returns vector with number of genes matched to any given pathway.
R Package Documentation
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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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