## ----style, echo=FALSE-------------------------------------------------------- knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE) library(BiocStyle) ## ----echo=FALSE, results='hide'----------------------------------------------- marker_names <- data.frame( full_name = c( "Carbonic anhydrase IX", "CD3 epsilon", "CD8 alpha", "E-Cadherin", "cleaved-Caspase3 + cleaved-PARP", "Cytokeratin 5", "Forkhead box P3", "Glucose transporter 1", "Histone H3", "phospho-Histone H3 [S28]", "Ki-67", "Myeloperoxidase", "Programmed cell death protein 1", "Programmed death-ligand 1", "phospho-Rb [S807/S811]", "Smooth muscle actin", "Vimentin", "Iridium 191", "Iridium 193" ), short_name = c( "CA9", "CD3e", "CD8a", "CDH1", "cCASP3_cPARP", "KRT5", "FOXP3", "SLC2A1", "H3", "p_H3", "Ki67", "MPO", "PD_1", "PD_L1", "p_Rb", "SMA", "VIM", "DNA1", "DNA2" ) ) ## ----echo=FALSE, results='asis'----------------------------------------------- knitr::kable( marker_names, caption = "'full_name' and 'short_name' examples for some commonly used markers" ) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()