## ----options, include = FALSE------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = NA, message=FALSE, warning=FALSE ) ## ----installation, eval=FALSE------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("immunogenViewer") ## ----load--------------------------------------------------------------------- library(immunogenViewer) ## ----get-features------------------------------------------------------------- protein <- getProteinFeatures("Q9NZC2") # check protein dataframe DT::datatable(protein, width = "80%", options = list(scrollX = TRUE)) ## ----add-immunogens----------------------------------------------------------- protein <- addImmunogen(protein, start = 142, end = 192, name = "ABIN2783734_") protein <- addImmunogen(protein, start = 196, end = 230, name = "HPA010917") protein <- addImmunogen(protein, seq = "HGQKPGTHPPSELD", name = "EB07921") # check that immunogens were added as columns colnames(protein) ## ----rename-immunogen--------------------------------------------------------- protein <- renameImmunogen(protein, oldName = "ABIN2783734_", newName = "ABIN2783734") # check that immunogen name was updated colnames(protein) ## ----remove-immunogen--------------------------------------------------------- protein <- removeImmunogen(protein, name = "HPA010917") # check that immunogen was removed colnames(protein) ## ----visualize_protein, fig.fullwidth=TRUE, fig.width=10, fig.height=10, out.width = "100%"---- plotProtein(protein) ## ----visualize_immunogen, fig.fullwidth=TRUE, fig.width=10, fig.height=10, out.width = "100%"---- plotImmunogen(protein, "ABIN2783734") ## ----evaluate----------------------------------------------------------------- immunogens <- evaluateImmunogen(protein) # check summary dataframe DT::datatable(immunogens, width = "80%", options = list(scrollX = TRUE)) ## ----sessioninfo-------------------------------------------------------------- sessionInfo()