TF_GSEA: A unified Gene Set Enrichment Analysis (GSEA) function for...
In lusystemsbio/NetAct: NetAct -- a computational platform to construct core transcription factor regulatory networks using gene activity
TF_GSEA R Documentation
A unified Gene Set Enrichment Analysis (GSEA) function for three methods
Description
A unified Gene Set Enrichment Analysis (GSEA) function for three methods
Usage
TF_GSEA(GSDB, DErslt, minSize = 5, nperm = 1000, method = "binary")
Arguments
GSDB
gene set database (a list of gene sets, each of which is comprised of a vector genes)
DErslt
DEG results
minSize
the minimum number of overlapping genes required for each gene set (a gene set filtering parameter, default: 5)
nperm
the number of gene list permutations (default: 1000)
method
fast: fgsea; r: R implementation of GSEA with a new permutation method; binary: R/C++ implementation for fast speed
Value
gseaRes: a table of GSEA results:
tf: TF (gene set name).
es: ES score.
lens: number of overlapping genes in each gene set.
pvals: p-value by counting.
z: z-score.
qvals: q-value from pvals.
lusystemsbio/NetAct documentation built on Sept. 7, 2024, 8:34 p.m.
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| TF_GSEA | R Documentation |
A unified Gene Set Enrichment Analysis (GSEA) function for three methods
Description
A unified Gene Set Enrichment Analysis (GSEA) function for three methods
Usage
TF_GSEA(GSDB, DErslt, minSize = 5, nperm = 1000, method = "binary")
Arguments
GSDB |
gene set database (a list of gene sets, each of which is comprised of a vector genes) |
DErslt |
DEG results |
minSize |
the minimum number of overlapping genes required for each gene set (a gene set filtering parameter, default: 5) |
nperm |
the number of gene list permutations (default: 1000) |
method |
fast: fgsea; r: R implementation of GSEA with a new permutation method; binary: R/C++ implementation for fast speed |
Value
gseaRes: a table of GSEA results: tf: TF (gene set name). es: ES score. lens: number of overlapping genes in each gene set. pvals: p-value by counting. z: z-score. qvals: q-value from pvals.
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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