getNMFGenes: Returns top module genes from NMF feature loading matrix
In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.
View source: R/utility_functions.R
getNMFGenes R Documentation
Returns top module genes from NMF feature loading matrix
Description
Returns top module genes from NMF feature loading matrix
Usage
getNMFGenes(feature.loading, norm.cutoff = 0.5)
Arguments
feature.loading
Matrix; m genes x n modules loading
norm.cutoff
Numeric [0,1]; cutoff to get top genes. Default is 0.5.
Author(s)
Nicholas Mikolajewicz
Examples
# get feature loading matrix (W matrix)
nmf.kme <- as.matrix(so.query@misc[["nmf"]][["nmf"]][["W"]])
# get module genes
nmf.module.genes <- getNMFGenes((nmf.kme), norm.cutoff = (1/ncol(nmf.kme)) + .25)
NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.
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View source: R/utility_functions.R
| getNMFGenes | R Documentation |
Returns top module genes from NMF feature loading matrix
Description
Returns top module genes from NMF feature loading matrix
Usage
getNMFGenes(feature.loading, norm.cutoff = 0.5)
Arguments
feature.loading |
Matrix; m genes x n modules loading |
norm.cutoff |
Numeric [0,1]; cutoff to get top genes. Default is 0.5. |
Author(s)
Nicholas Mikolajewicz
Examples
# get feature loading matrix (W matrix)
nmf.kme <- as.matrix(so.query@misc[["nmf"]][["nmf"]][["W"]])
# get module genes
nmf.module.genes <- getNMFGenes((nmf.kme), norm.cutoff = (1/ncol(nmf.kme)) + .25)
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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