SMPDB2Gmat: Transform SMPDB protein and/or metabolite pathway data frames...
In jdreyf/PANTS: Pathway analysis via network smoothing
Description
Usage
Arguments
Value
Description
Transform SMPDB protein and/or metabolite pathway data frames, read in as CSV files from http://smpdb.ca/downloads,
into a pathway matrix that matches Pathway Commons, using Gene.Name to identify proteins and ChEBI IDs for metabolites.
Format of SMPDB downloads has changed, so now it has numerous semi-redundant fatty acid pathways, so this will need to
be modified if want to stay up to date with SMPDB.
Usage
1
SMPDB2Gmat(smpdb.prot, smpdb.met, exclude.pwy.subj = NA)
Arguments
smpdb.prot
Data frame of proteins per pathway from SMPDB.
smpdb.met
Data frame of metabolites per pathway from SMPDB.
exclude.pwy.subj
Vector of subjects (or types) of pathways to exclude
Value
A numeric Matrix of features (proteins and/or metabolites) as rows and pathways as columns, indicating
pathway membership.
jdreyf/PANTS documentation built on July 18, 2019, 10:12 a.m.
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Description Usage Arguments Value
Description
Transform SMPDB protein and/or metabolite pathway data frames, read in as CSV files from http://smpdb.ca/downloads, into a pathway matrix that matches Pathway Commons, using Gene.Name to identify proteins and ChEBI IDs for metabolites. Format of SMPDB downloads has changed, so now it has numerous semi-redundant fatty acid pathways, so this will need to be modified if want to stay up to date with SMPDB.
Usage
1 | SMPDB2Gmat(smpdb.prot, smpdb.met, exclude.pwy.subj = NA)
|
Arguments
smpdb.prot |
Data frame of proteins per pathway from SMPDB. |
smpdb.met |
Data frame of metabolites per pathway from SMPDB. |
exclude.pwy.subj |
Vector of subjects (or types) of pathways to exclude |
Value
A numeric Matrix of features (proteins and/or metabolites) as rows and pathways as columns, indicating pathway membership.
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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