## ----eval = FALSE------------------------------------------------------------- # # for bioconductor # if (!require("BiocManager")) # install.packages("BiocManager") # # BiocManager::install("tomoseqr") ## ----setup, message = FALSE--------------------------------------------------- library(tomoseqr) ## ----------------------------------------------------------------------------- data(testx, testy, testz) head(testx) ## ---- eval = FALSE------------------------------------------------------------ # tomoCache <- downloadJunker2014() # junker2014 <- doadJunker2014(tomoCache) # # sheldAV <- junker2014[["sheldAV"]] # sheldVD <- junker2014[["sheldVD"]] # sheldLR <- junker2014[["sheldLR"]] # mask <- junker2014[["mask"]] ## ----------------------------------------------------------------------------- data(mask) ## ----eval = FALSE------------------------------------------------------------- # masker() ## ----------------------------------------------------------------------------- tomoObj <- estimate3dExpressions( testx, testy, testz, mask = mask, query = c("gene1", "gene2", "gene3") ) ## ----eval = FALSE------------------------------------------------------------- # imageViewer(tomoObj, geneID = "gene3") ## ----------------------------------------------------------------------------- axialGeneTable <- findAxialGenes(testx) print(axialGeneTable) ## ----------------------------------------------------------------------------- axialGeneTable <- findAxialGenes(testx, genes = c("gene1", "gene3")) print(axialGeneTable) ## ----------------------------------------------------------------------------- sessionInfo()