## ----, env, eval=TRUE, echo=FALSE, warning=FALSE, message=FALSE---------- library(knitcitations) cite_options(hyperlink = FALSE, style = "markdown") library(bibtex) extbib <- read.bib("pRolocGUI.bib") ## ----, echo = TRUE, message = FALSE, warning = FALSE--------------------- library("pRolocGUI") data(andy2011, package = "pRolocdata") data(tan2009r1, package = "pRolocdata") data(tan2009r2, package = "pRolocdata") data(dunkley2006, package = "pRolocdata") ## ----, eval = FALSE, echo = TRUE----------------------------------------- ## pRolocVis(object = andy2011) ## ----, eval = FALSE, echo = TRUE----------------------------------------- ## namedVis <- list(andy2011 = andy2011, tan2009r1 = tan2009r1, dunkley2006 = dunkley2006) ## unnamedVis <- list(andy2011, tan2009r1, dunkley2006) ## pRolocVis(object = namedVis) ## pRolocVis(object = unnamedVis) ## ----, eval = FALSE, echo = TRUE----------------------------------------- ## namedComp <- list(tan2009r1 = tan2009r1, tan2009r2 = tan2009r2) ## unnamedComp <- list(tan2009r1, tan2009r2) ## pRolocComp(object = namedComp) ## pRolocComp(object = unnamedComp) ## ----, eval = TRUE, echo = TRUE------------------------------------------ data(tan2009r1, package = "pRolocdata") pRolocGUI_SearchResults <- FoICollection() newFeat <- FeaturesOfInterest(description = "test_01", fnames = featureNames(tan2009r1)[1:10], object = tan2009r1) pRolocGUI_SearchResults <- addFeaturesOfInterest(newFeat, pRolocGUI_SearchResults) ## ----, eval = TRUE, echo = TRUE------------------------------------------ data(tan2009r1, package = "pRolocdata") data(tan2009r2, package = "pRolocdata") featcomp <- compfnames(x = tan2009r1, y = tan2009r2, fcol1 = "markers", fcol2 = "markers", verbose = FALSE) ## the fourth element in the list bears information about features which are assigned to ## "mitochondrion" in "markers", we can access all common features for tan2009r1 and tan2009r2 by feat <- slot(featcomp[[4]], "common") feat ## ----, results="asis", message=FALSE, echo=FALSE------------------------- bibliography()