expand_KEGG_mappings: Get detailed KEGG mapping information for each map entity
In shanawhite-UC/KEGGlincs: Visualize all edges within a KEGG pathway and overlay LINCS data
Description
Usage
Arguments
Value
Examples
Description
Extract mapping information from KGML object and normalize
mappings based on multi-valued name attribute
Usage
1
expand_KEGG_mappings(KGML_file, convert_KEGG_IDs = TRUE)
Arguments
KGML_file
An object of formal class KEGGPathway
convert_KEGG_IDs
A logical indicator; if set to FALSE will run faster
however genes and compounds will remain labeled via KEGG codes (compounds)
or accession numbers (genes). This option must be taken into account if
data is being added. For example, the genes in 'KO_data' are identified by
symbols, thus it is neccessary to retain the default option to convert IDs
to symbols when planning to add edge data of this type.
Value
A dataframe object with unique entry information for all [node]
objects documented in the KEGG pathway.
Note that if mutiple objects (i.e. genes or compounds) have the same
entryID, this indicates that they share the same node [location]
in the pathway.
Examples
1
2
p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML, FALSE)
shanawhite-UC/KEGGlincs documentation built on May 29, 2019, 8:07 p.m.
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Description Usage Arguments Value Examples
Description
Extract mapping information from KGML object and normalize mappings based on multi-valued name attribute
Usage
1 | expand_KEGG_mappings(KGML_file, convert_KEGG_IDs = TRUE)
|
Arguments
KGML_file |
An object of formal class KEGGPathway |
convert_KEGG_IDs |
A logical indicator; if set to FALSE will run faster however genes and compounds will remain labeled via KEGG codes (compounds) or accession numbers (genes). This option must be taken into account if data is being added. For example, the genes in 'KO_data' are identified by symbols, thus it is neccessary to retain the default option to convert IDs to symbols when planning to add edge data of this type. |
Value
A dataframe object with unique entry information for all [node] objects documented in the KEGG pathway. Note that if mutiple objects (i.e. genes or compounds) have the same entryID, this indicates that they share the same node [location] in the pathway.
Examples
1 2 | p53_KGML <- get_KGML("hsa04115")
p53_KEGG_mappings <- expand_KEGG_mappings(p53_KGML, FALSE)
|
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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