getPCRsizes: getPCRsizes

In dianalow/SPLINTER: Splice Interpreter of Transcripts

getPCRsizes

Description

returns length of product given a GRanges span and GRangesList of transcripts

Usage

getPCRsizes(pcr_span, txlist, verbose = FALSE)

Arguments

pcr_span	GRanges object
txlist	GRangesList object
verbose	logical. report intermediate output.

Value

data.frame of transcript names with detected sizes in basepairs

Author(s)

Diana Low

Examples

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)

dianalow/SPLINTER documentation built on March 28, 2024, 2:07 p.m.