GEM matlab file from Chalmers Sysbio (Wang et al., 2021)
Source:R/chalmers_gem.R
chalmers_gem_raw.RdDownloads and imports the matlab file containing the genome scale metabolic models created by Chalmers SysBio.
Details
The Matlab object is parsed into a nested list containing a number of vectors and two sparse matrices. The top level contains a single element under the name "ihuman" for human; under this key there is an array of 31 elements. These elements are labeled by the row names of the array.
References
Wang H, Robinson JL, Kocabas P, Gustafsson J, Anton M, Cholley PE, Huang S, Gobom J, Svensson T, Uhlen M, Zetterberg H, Nielsen J. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. Proc Natl Acad Sci U S A. 2021 Jul 27;118(30):e2102344118. doi: doi:10.1073/pnas.2102344118 .
Examples
chalmers_gem_raw()
#> $ihuman
#> , , 1
#>
#> [,1]
#> id "Human-GEM"
#> description "Generic genome-scale metabolic model of Homo sapiens"
#> rxns list,12995
#> mets list,8456
#> S <S4 class ‘dgCMatrix’ [package “Matrix”] with 6 slots>
#> lb numeric,12995
#> ub numeric,12995
#> rev numeric,12995
#> c numeric,12995
#> b numeric,8456
#> comps list,9
#> compNames list,9
#> rxnNames list,12995
#> grRules list,12995
#> rxnGeneMat <S4 class ‘dgCMatrix’ [package “Matrix”] with 6 slots>
#> subSystems list,12995
#> eccodes list,12995
#> rxnNotes list,12995
#> genes list,2889
#> geneShortNames list,2889
#> metNames list,8456
#> metComps numeric,8456
#> inchis list,8456
#> metFormulas list,8456
#> rxnReferences list,12995
#> rxnFrom list,12995
#> metFrom list,8456
#> rxnConfidenceScores numeric,12995
#> metCharges numeric,8456
#> version "1.18.0"
#> annotation list,5
#>
#>
#> attr(,"header")
#> attr(,"header")$description
#> [1] "MATLAB 5.0 MAT-file, Platform: MACI64, Created on: Fri Dec 8 14:17:06 2023 "
#>
#> attr(,"header")$version
#> [1] "5"
#>
#> attr(,"header")$endian
#> [1] "little"
#>
#> attr(,"origin")
#> [1] "cache"
#> attr(,"resource")
#> [1] "Chalmers GEM"
#> attr(,"url")
#> [1] "https://raw.githubusercontent.com/SysBioChalmers/Human-GEM/main/model/Human-GEM.mat"
#> attr(,"source")
#> [1] "Chalmers GEM (raw.githubusercontent.com)"