gmt_to_list: convert gmt format of pathways to list of vectors
In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters
Description
Usage
Arguments
Value
Examples
Description
convert gmt format of pathways to list of vectors
Usage
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gmt_to_list(
path,
cutoff = 0,
sep = "\thttp://www.broadinstitute.org/gsea/msigdb/cards/.*?\t"
)
Arguments
path
gmt file path
cutoff
remove pathways with less genes than this cutoff
sep
sep used in file to split path and genes
Value
list of genes in each pathway
Examples
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gmt_file <- system.file(
"extdata",
"c2.cp.reactome.v6.2.symbols.gmt.gz",
package = "clustifyr"
)
gl <- gmt_to_list(path = gmt_file)
length(gl)
clustifyr documentation built on Nov. 8, 2020, 5:32 p.m.
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Description Usage Arguments Value Examples
Description
convert gmt format of pathways to list of vectors
Usage
1 2 3 4 5 | gmt_to_list(
path,
cutoff = 0,
sep = "\thttp://www.broadinstitute.org/gsea/msigdb/cards/.*?\t"
)
|
Arguments
path |
gmt file path |
cutoff |
remove pathways with less genes than this cutoff |
sep |
sep used in file to split path and genes |
Value
list of genes in each pathway
Examples
1 2 3 4 5 6 7 8 | gmt_file <- system.file(
"extdata",
"c2.cp.reactome.v6.2.symbols.gmt.gz",
package = "clustifyr"
)
gl <- gmt_to_list(path = gmt_file)
length(gl)
|
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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