## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", crop = NULL ## Related to https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html ) ## ---- eval = FALSE------------------------------------------------------------ # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("BioPlex") ## ---- message = FALSE--------------------------------------------------------- library(BioPlex) library(AnnotationHub) library(ExperimentHub) library(graph) ## ----ahub, message = FALSE---------------------------------------------------- ah <- AnnotationHub::AnnotationHub() ## ----ehub, message = FALSE---------------------------------------------------- eh <- ExperimentHub::ExperimentHub() ## ----orgdb, message = FALSE--------------------------------------------------- orgdb <- AnnotationHub::query(ah, c("orgDb", "Homo sapiens")) orgdb <- orgdb[[1]] orgdb keytypes(orgdb) ## ----bioplex293T-------------------------------------------------------------- bp.293t <- getBioPlex(cell.line = "293T", version = "3.0") head(bp.293t) nrow(bp.293t) ## ----bioplexHCT116------------------------------------------------------------ bp.hct116 <- getBioPlex(cell.line = "HCT116", version = "1.0") head(bp.hct116) nrow(bp.hct116) ## ----bioplex-remap------------------------------------------------------------ bp.293t.remapped <- getBioPlex(cell.line = "293T", version = "3.0", remap.uniprot.ids = TRUE) ## ----bpgraph------------------------------------------------------------------ bp.gr <- bioplex2graph(bp.293t) bp.gr head(graph::nodeData(bp.gr)) head(graph::edgeData(bp.gr)) ## ----pfam--------------------------------------------------------------------- bp.gr <- annotatePFAM(bp.gr, orgdb) head(graph::nodeData(bp.gr, graph::nodes(bp.gr), "PFAM")) ## ----corumALL----------------------------------------------------------------- all <- getCorum(set = "all", organism = "Human") dim(all) colnames(all) all[1:5, 1:5] ## ----corumCore---------------------------------------------------------------- core <- getCorum(set = "core", organism = "Human") dim(core) ## ----corumSplice-------------------------------------------------------------- splice <- getCorum(set = "splice", organism = "Human") dim(splice) ## ----corum-remap-------------------------------------------------------------- core.remapped <- getCorum(set = "core", organism = "Human", remap.uniprot.ids = TRUE) ## ----corum2list--------------------------------------------------------------- core.list <- corum2list(core, subunit.id.type = "UNIPROT") head(core.list) length(core.list) ## ----corum2glist-------------------------------------------------------------- core.glist <- corum2graphlist(core, subunit.id.type = "UNIPROT") head(core.glist) length(core.glist) core.glist[[1]]@graphData graph::nodeData(core.glist[[1]]) ## ----gse122425---------------------------------------------------------------- se <- getGSE122425() se head(assay(se, "raw")) head(assay(se, "rpkm")) colData(se) rowData(se) ## ---- eval = FALSE------------------------------------------------------------ # ccle.trans <- ExpressionAtlas::getAtlasExperiment("E-MTAB-2770") ## ---- eval = FALSE------------------------------------------------------------ # klijn <- ExpressionAtlas::getAtlasExperiment("E-MTAB-2706") ## ----ccle-proteom------------------------------------------------------------- AnnotationHub::query(eh, c("gygi", "depmap")) ccle.prot <- eh[["EH3459"]] ccle.prot <- as.data.frame(ccle.prot) ## ----ccle-proteom2------------------------------------------------------------ dim(ccle.prot) colnames(ccle.prot) head(ccle.prot) ## ----ccle-prot-hct116--------------------------------------------------------- ccle.prot.hct116 <- subset(ccle.prot, cell_line == "HCT116_LARGE_INTESTINE") dim(ccle.prot.hct116) head(ccle.prot.hct116) ## ----ccle-prot-se------------------------------------------------------------- se <- ccleProteome2SummarizedExperiment(ccle.prot, cell.line = NULL) assay(se)[1:5, 1:5] assay(se)[1:5, "HCT116"] rowData(se) ## ----bp.prot------------------------------------------------------------------ bp.prot <- getBioplexProteome() assay(bp.prot)[1:5,1:5] colData(bp.prot) rowData(bp.prot) ## ----cache-------------------------------------------------------------------- cache.dir <- tools::R_user_dir("BioPlex", which = "cache") bfc <- BiocFileCache::BiocFileCache(cache.dir) ## ----rmCache, eval = FALSE---------------------------------------------------- # BiocFileCache::removebfc(bfc) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()