getPCRsizes {SPLINTER} | R Documentation

## 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)

[Package SPLINTER version 1.13.3 Index]