clean_pathways: Clean the pathways or feature sets provided by the user
In LucaGiudice/Simpati: Pathway-based classifier exploits patient similarity network paradigm
Description
Usage
Arguments
Value
Description
Maps the feature names of the matrix of patient's profiles to the corresponding name in the feature sets/pathway
Plus, it removes all the feature sets mapping only few existing features (defined by: dim_pathway parameter)
Usage
1
clean_pathways(pathways_l, geno, size = 4, n_cores = 2)
Arguments
geno
Matrix of profiles (genes x samples)
n_cores
Number greater than 1 indicating the number of cores for parallel computing
pathwayList
List of gene sets
dim_pathway
Number greater than 1 indicating the minimum size of the pathways
Value
Filtered and indexes pathways/feature sets
LucaGiudice/Simpati documentation built on Jan. 27, 2022, 11:42 p.m.
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Description Usage Arguments Value
Description
Maps the feature names of the matrix of patient's profiles to the corresponding name in the feature sets/pathway Plus, it removes all the feature sets mapping only few existing features (defined by: dim_pathway parameter)
Usage
1 | clean_pathways(pathways_l, geno, size = 4, n_cores = 2)
|
Arguments
geno |
Matrix of profiles (genes x samples) |
n_cores |
Number greater than 1 indicating the number of cores for parallel computing |
pathwayList |
List of gene sets |
dim_pathway |
Number greater than 1 indicating the minimum size of the pathways |
Value
Filtered and indexes pathways/feature sets
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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