get_TME_genes: Extract TME genes from methylation expression clustering
In tanaylab/methylayer: Layered modeling of tumor methylation
Description
Usage
Arguments
Value
Description
Extracts names of genes that were clustered together with canonical immune and CAF genes in the expression-methylation correlation matrix. This is used mostly for filtering those genes from additional analysis such as cis-regulation.
Usage
1
get_TME_genes(em_list, immune_gene = "CD3D", caf_gene = "CAV1")
Arguments
em_list
output of em_cross_cor
immune_gene
name of canonical immune gene (default: CD3D). If NULL - only CAF genes would be returned.
caf_gene
name of canonical immune gene (default: CAV1). If NULL - only immune genes would be returned.
Value
vector with names of TME genes
tanaylab/methylayer documentation built on Dec. 23, 2021, 7:45 a.m.
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Description Usage Arguments Value
Description
Extracts names of genes that were clustered together with canonical immune and CAF genes in the expression-methylation correlation matrix. This is used mostly for filtering those genes from additional analysis such as cis-regulation.
Usage
1 | get_TME_genes(em_list, immune_gene = "CD3D", caf_gene = "CAV1")
|
Arguments
em_list |
output of |
immune_gene |
name of canonical immune gene (default: CD3D). If NULL - only CAF genes would be returned. |
caf_gene |
name of canonical immune gene (default: CAV1). If NULL - only immune genes would be returned. |
Value
vector with names of TME genes
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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