## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set( collapse=TRUE, comment="#>", warning=FALSE, error=FALSE, crop = NULL ) ## ----library, message=FALSE, warning=FALSE, error=FALSE----------------------- library(BiocStyle) library(HPAanalyze) library(dplyr) ## ----hpaVis_eg---------------------------------------------------------------- hpaVis(targetGene = c("GCH1", "PTS", "SPR", "DHFR"), targetTissue = c("cerebellum", "cerebral cortex", "hippocampus"), targetCancer = c("glioma")) ## ----hpaVis_eg2, eval = FALSE------------------------------------------------- # hpaVis() # # # No data provided. Use version ... # # targetGene variable not specified, default to TP53, RB1, MYC, KRAS and EGFR. # # targetTissue variable not specified, default to breast. # # targetCellType variable not specified, visualize all. # # * WARNING: targetCellType variable not specified, visualize all. # # >> Use hpaListParam() to list possible values for target variables. # # targetCancer variable not specified, default to breast cancer # # Use hpaListParam() to list possible values for target variables. # ## ----hpaVis_eg3--------------------------------------------------------------- hpaVis(visType = "Patho", targetGene = c("GCH1", "PTS", "SPR", "DHFR"), targetCancer = c("glioma", "breast cancer")) ## ----hpaVisPatho_eg----------------------------------------------------------- hpaVisPatho(targetGene = c("GCH1", "PTS", "SPR", "DHFR")) ## ----doc_ex1, eval = FALSE---------------------------------------------------- # ?hpaVis # the easy umbrella to visualize protein expression levels # ?hpaVisTissue # in normal tissue # ?hpaVisSubcell # in subcellular compartments # ?hpaVisPatho # in cancers ## ----listParam_ex, eval = FALSE----------------------------------------------- # hpaListParam() ## ----listParam_ex2, echo= FALSE----------------------------------------------- hpaListParam() %>% glimpse() ## ----eval=FALSE--------------------------------------------------------------- # EGFR <- hpaXml(inputXml='ENSG00000146648') # names(EGFR) # # #> [1] "ProtClass" "TissueExprSum" "Antibody" "TissueExpr" ## ----doc_ex2, eval = FALSE---------------------------------------------------- # ?hpaXmlGet # import the xml file as "xml_document" # ?hpaXmlProtClass # ?hpaXmlTissueExprSum # ?hpaXmlAntibody # ?hpaXmlTissueExpr