getPCRsizes {SPLINTER} | R Documentation |
returns length of product given a GRanges span and GRangesList of transcripts
getPCRsizes(pcr_span, txlist, verbose = FALSE)
pcr_span |
GRanges object |
txlist |
GRangesList object |
verbose |
logical. report intermediate output. |
data.frame of transcript names with detected sizes in basepairs
Diana Low
suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9)) bsgenome<-BSgenome.Mmusculus.UCSC.mm9 ## create a primer pair ## for actual use, obtain primer pair from primer design (callPrimer3) primer_pair <- data.frame(PRIMER_LEFT_SEQUENCE="agctcttgaaattggagctgac", PRIMER_RIGHT_SEQUENCE="cttagaaagaacaggaaatcc", stringsAsFactors=FALSE) ## confirm location cp<-checkPrimer(primer_pair,bsgenome,roi) cp ## get the PCR sizes pcr_result1 <- getPCRsizes(cp,theexons)