Package 'pathview' - Bioconductor

26 sim.mol.datahead(pv.out$plot.data.cpd)#result PNG file in current directory##more examples of pathview usages are shown in the vignette.sim.mol.dataSimulate molecular data for pathview experimentDescriptionUsageThe molecular data simulator generates either gene.data or cpd.data of different ID types, moleculenumbers, sample sizes, either continuous or discrete.sim.mol.data(mol.type = c("gene", "gene.ko", "cpd")[1], id.type = NULL,species="hsa", discrete = FALSE, nmol = 1000, nexp = 1, rand.seed=100)Argumentsmol.typeid.typespeciesdiscretenmolnexprand.seedcharacter of length 1, specifing the molecular type, either "gene" (including transcripts,proteins), or "gene.ko" (KEGG ortholog genes, as defined in KEGG orthologpathways), or "cpd" (including metabolites, glycans, drugs). Note thatKEGG ortholog gene are considered "gene" in function pathview. Defaultmol.type="gene".character of length 1, the molecular ID type. When mol.type="gene", proper IDtypes include "KEGG" and "ENTREZ" (Entrez Gene). Other ID types are alsovalid When species="hsa" only, check:data(gene.idtype.list); gene.idtype.list for other valid ID types. Whenmol.type="cpd", check data(cpd.simtypes); cpd.simtypes for valid IDtypes. Default id.type=NULL, then "Entrez" and "KEGG COMPOUND accession"will be assumed for mol.type = "gene" or "cpd".character, either the kegg code, scientific name or the common name of the targetspecies. This is only effective when mol.type = "gene". Setting species="ko"is equilvalent to mol.type="gene.ko". Default species="hsa", equivalent to either"Homo sapiens" (scientific name) or "human" (common name), gene dataid.type has multiple other choices. When other species are specified, geneid.type is limited to "KEGG" and "ENTREZ".logical, whether to generate discrete or continuous data. d discrete=FALSE,otherwise, mol.data will be a charactor vector of molecular IDs.integer, the target number of different molecules. Note that the specified id.typemay not have as many different IDs as nmol. In this case, all IDs of id.type areused.integer, the sample size or the number of columns in the result simulated data.numeric of length 1, the seed number to start the random sampling process.This argumemnt makes the simulation reproducible as long as its value keepsthe same. Default rand.seed=100.