## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( comment = "#>", collapse = TRUE, message = FALSE, warning = FALSE, fig.align='center' ) ## ----eval = FALSE------------------------------------------------------------- # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("GenomicSuperSignature") # BiocManager::install("bcellViper") ## ----results="hide", message=FALSE, warning=FALSE----------------------------- library(GenomicSuperSignature) library(bcellViper) ## ----load_model--------------------------------------------------------------- RAVmodel <- getModel("PLIERpriors", load=TRUE) RAVmodel version(RAVmodel) ## ----message=FALSE, warning=FALSE--------------------------------------------- data(bcellViper) dset ## ----------------------------------------------------------------------------- val_all <- validate(dset, RAVmodel) head(val_all) ## ----out.height="80%", out.width="80%", message=FALSE, warning=FALSE---------- heatmapTable(val_all, RAVmodel, num.out = 5, swCutoff = 0) ## ----out.height="75%", out.width="75%", plotValidate_function----------------- plotValidate(val_all, interactive = FALSE) ## ----------------------------------------------------------------------------- validated_ind <- validatedSignatures(val_all, RAVmodel, num.out = 3, swCutoff = 0, indexOnly = TRUE) validated_ind ## ----out.height="60%", out.width="60%"---------------------------------------- set.seed(1) # only if you want to reproduce identical display of the same words drawWordcloud(RAVmodel, validated_ind[1]) drawWordcloud(RAVmodel, validated_ind[2]) drawWordcloud(RAVmodel, validated_ind[3]) ## ----------------------------------------------------------------------------- annotateRAV(RAVmodel, validated_ind[2]) # RAV1139 ## ----------------------------------------------------------------------------- subsetEnrichedPathways(RAVmodel, validated_ind[2], include_nes = TRUE) subsetEnrichedPathways(RAVmodel, validated_ind, include_nes = TRUE) ## ----------------------------------------------------------------------------- findSignature(RAVmodel, "Bcell") ## ----------------------------------------------------------------------------- findSignature(RAVmodel, "Bcell", k = 5) ## ----------------------------------------------------------------------------- findKeywordInRAV(RAVmodel, "Bcell", ind = 695) ## ----------------------------------------------------------------------------- ## Chosen based on validation/MeSH terms subsetEnrichedPathways(RAVmodel, ind = validated_ind[2], n = 3, both = TRUE) ## Chosen based on enriched pathways subsetEnrichedPathways(RAVmodel, ind = 695, n = 3, both = TRUE) subsetEnrichedPathways(RAVmodel, ind = 953, n = 3, both = TRUE) subsetEnrichedPathways(RAVmodel, ind = 1994, n = 3, both = TRUE) ## ----------------------------------------------------------------------------- findStudiesInCluster(RAVmodel, validated_ind[2]) ## ----------------------------------------------------------------------------- findStudiesInCluster(RAVmodel, validated_ind[2], studyTitle = TRUE) ## ----------------------------------------------------------------------------- sessionInfo()