## ----style, include = FALSE, results = 'asis'--------------------------------- BiocStyle::html_document() ## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, dpi=200 ) library(kableExtra) ## ----message=FALSE------------------------------------------------------------ library(MetaPhOR) ## ----------------------------------------------------------------------------- exdegs <- read.csv(system.file("extdata/exampledegs.csv", package = "MetaPhOR"), header = TRUE) ## ----echo=FALSE--------------------------------------------------------------- kable(head(exdegs), format="html") %>% kable_material() ## ----include=FALSE------------------------------------------------------------ # BRCA, OVCA, PRAD # sampsize <- c(1095, 378, 497) ## ----------------------------------------------------------------------------- set.seed(1234) brca <- pathwayAnalysis(DEGpath = system.file("extdata/BRCA_DEGS.csv", package = "MetaPhOR"), genename = "X", sampsize = 1095, iters = 50000, headers = c("logFC", "adj.P.Val")) ## ----echo = FALSE------------------------------------------------------------- kable(head(brca), format="html", booktabs = TRUE) %>% kable_material() ## ----------------------------------------------------------------------------- pval <- bubblePlot(scorelist = brca, labeltext = "Pval", labelsize = .85) plot(pval) ## ----------------------------------------------------------------------------- logfc <- bubblePlot(scorelist = brca, labeltext = "LogFC", labelsize = .85) plot(logfc) ## ----------------------------------------------------------------------------- ##read in two additional sets of scores, ##run in the same manner as brca for comparison ovca <- read.csv(system.file("extdata/OVCA_Scores.csv", package = "MetaPhOR"), header = TRUE, row.names = 1) prad <- read.csv(system.file("extdata/PRAD_Scores.csv", package = "MetaPhOR"), header = TRUE, row.names = 1) all.scores <- list(brca, ovca, prad) names <- c("BRCA", "OVCA", "PRAD") metaHeatmap(scorelist = all.scores, samplenames = names, pvalcut = 0.05) ## ----eval = FALSE------------------------------------------------------------- # cytoPath(pathway = "Tryptophan Metabolism", # DEGpath = "BRCA_DEGS.csv", # figpath = paste(getwd(), "BRCA_Tryptophan_Pathway", sep = "/"), # genename = "X", # headers = c("logFC", "adj.P.Val")) ## ----echo = F, fig.wide = TRUE------------------------------------------------ knitr::include_graphics(c(system.file("extdata", "BRCA_Tryptophan_Pathway.png", package = "MetaPhOR"))) ## ----eval = FALSE------------------------------------------------------------- # pathwayList() ## ----echo = F----------------------------------------------------------------- kable(head(pathwayList()), format = "html", booktabs = TRUE) %>% kable_material() ## ----------------------------------------------------------------------------- sessionInfo()