## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set(collapse=TRUE) ## ----loaddata, message=F,warning=F-------------------------------------------- library("annotate") library("hu6800.db") lens <- unlist(eapply(hu6800CHR, length)) table(lens) wh2 = mget(names(lens)[lens==2], env = hu6800CHR) wh2[1] ## ----fixdata------------------------------------------------------------------ chrs2 <- unlist(eapply(hu6800CHR, function(x) x[1])) chrs2 <- factor(chrs2) length(chrs2) table(unlist(chrs2)) ## ----strandloc---------------------------------------------------------------- strand <- as.list(hu6800CHRLOC) splits <- split(strand, chrs2) length(splits) names(splits) ## ----chrloc------------------------------------------------------------------- newChrClass <- buildChromLocation("hu6800") ## ----cPlot, fig=TRUE---------------------------------------------------------- library(geneplotter) ## Reorder Chromosomes newChrClass@chromLocs <- newChrClass@chromLocs[order(as.numeric(names(newChrClass@chromLocs)))] newChrClass@chromInfo <- newChrClass@chromInfo[order(as.numeric(names(newChrClass@chromInfo)))] cPlot(newChrClass,useChroms = as.character(c(names(splits),"X","Y","M")))