## ----style, echo = FALSE, results = 'asis', warnings=FALSE, messages=FALSE---- BiocStyle::markdown() ## ----setup, include=FALSE-------------------------------------------------- knitr::opts_chunk$set(cache=FALSE) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- library("DNABarcodes") mySet <- create.dnabarcodes(5) show(mySet) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- mySetAshlock <- create.dnabarcodes(5, heuristic="ashlock") show(mySetAshlock) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- mySetDist5 <- create.dnabarcodes(5, dist=5, heuristic="ashlock") show(mySetDist5) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- show(length(create.dnabarcodes(5, dist=5, heuristic="ashlock"))) show(length(create.dnabarcodes(6, dist=5, heuristic="ashlock"))) show(length(create.dnabarcodes(7, dist=5, heuristic="ashlock"))) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- mySeqlevSet <- create.dnabarcodes(5, metric="seqlev", heuristic="ashlock") show(mySeqlevSet) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- mySetTriplets <- create.dnabarcodes(5, heuristic="ashlock", filter.triplets=FALSE) show(mySetTriplets) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- data(supplierSet) myRobustSet <- create.dnabarcodes(7, dist=5, pool=supplierSet, heuristic="ashlock") show(myRobustSet) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- myRobustSetSeqlev <- create.dnabarcodes(7, metric="seqlev", pool=supplierSet, heuristic="ashlock") show(myRobustSetSeqlev) ## ----eval=TRUE, collapse=TRUE---------------------------------------------- data(mutatedReads) demultiplex(head(mutatedReads), supplierSet) ## ----eval=TRUE,collapse=TRUE----------------------------------------------- analyse.barcodes(supplierSet) ## ----eval=FALSE, collapse=TRUE--------------------------------------------- # length(create.dnabarcodes(10, metric="seqlev", heuristic="ashlock",cores=32)) # ## 1) Creating pool ... of size 488944 # ## 2) Initiating Chromosomes done # ## 3) Running Greedy Evolutionary done # ## 2126 # length(create.dnabarcodes(10, metric="seqlev", heuristic="ashlock",cores=32, population=500, iterations=250)) # ## 1) Creating pool ... of size 488944 # ## 2) Initiating Chromosomes done # ## 3) Running Greedy Evolutionary done # ## 2133