sc_geneset_enrich: Geneset Enrichment (GSE) on scRNAseq Data Calculates single...
In tolgaturan-github/IBRIDGE: IBRIDGE integrates bulk and single-cell datasets to profile granular heterogeneity of TIME, acting as a 'bridge' between data types.
View source: R/geneset_enrichment.R
sc_geneset_enrich R Documentation
Geneset Enrichment (GSE) on scRNAseq Data
Calculates single cell GSE scores using "AUCell" method
Description
Geneset Enrichment (GSE) on scRNAseq Data
Calculates single cell GSE scores using "AUCell" method
Usage
sc_geneset_enrich(seu1, geneset_list, norm_method = "SCTransform", n_cores = 1)
Arguments
seu1
Output of UMI count matrix normalized by Seurat workflows
geneset_list
a List of gene/Transcript features.
Preferably all or at least 1 feature in each geneset must be present in the rownames of the expression matrix.
norm_method
"SCTransform" or "NormalizeData". Defaults to "SCTransform"
n_cores
Integer of length 1. Specifies the number of parallel cores running the function.
Defaults to 1
Value
data.frame holding geneset enrichment values for each geneset (columns) and for each cell (rows).
Author(s)
Tolga Turan, tolga.turan@abbvie.com
References
http://github.com/tolgaturan-github/IBRIDGE
Examples
enrichment_scores1<-sc_geneset_enrich(seu1, geneset_list1, "SCTransform", 100)
tolgaturan-github/IBRIDGE documentation built on July 30, 2023, 12:08 p.m.
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View source: R/geneset_enrichment.R
| sc_geneset_enrich | R Documentation |
Geneset Enrichment (GSE) on scRNAseq Data Calculates single cell GSE scores using "AUCell" method
Description
Geneset Enrichment (GSE) on scRNAseq Data Calculates single cell GSE scores using "AUCell" method
Usage
sc_geneset_enrich(seu1, geneset_list, norm_method = "SCTransform", n_cores = 1)
Arguments
seu1 |
Output of UMI count matrix normalized by Seurat workflows |
geneset_list |
a List of gene/Transcript features. Preferably all or at least 1 feature in each geneset must be present in the rownames of the expression matrix. |
norm_method |
"SCTransform" or "NormalizeData". Defaults to "SCTransform" |
n_cores |
Integer of length 1. Specifies the number of parallel cores running the function. Defaults to 1 |
Value
data.frame holding geneset enrichment values for each geneset (columns) and for each cell (rows).
Author(s)
Tolga Turan, tolga.turan@abbvie.com
References
http://github.com/tolgaturan-github/IBRIDGE
Examples
enrichment_scores1<-sc_geneset_enrich(seu1, geneset_list1, "SCTransform", 100)
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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