testPrimer: Give Mutiple primers,test the amplication sequence and...

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

Give Mutiple primers,test the amplication sequence and whether cross different exons

Usage

testPrimer(forward, reverse, path.transcript.fa = NULL,
  path.exon.fa = NULL, verbose = T)

Arguments

forward	a name vector of forward primers
reverse	a name vector of reverse primers
path.transcript.fa	the path of transcript(cDNA) fa file.if primers are multiple,it is recommanded to set path.transcript.fa=NULL
path.exon.fa	the path of exons fa file.if primers are multiple,it is recommanded to set path.exon.fa=NULL

Value

A luckyList

Author(s)

Weibin Huang<[e-mail]>

See Also

XStringSet-io;XVector-class;matchPattern;testPrimer1

Examples

library(lucky)
forward = c(DSCR8="GGGTGGCAAAAAGAGAAGATGG",
            DSCR8 = "CGTCTTGTCCACTCGTTTCTG",
            DSCR8 = "AAATAGGCTTCCCACTTGGC",
            DSCR8 = "GGGTGGCAAAAAGAGAAGATGG")
reverse = c(DSCR8="GGTCCAGGCTCCTTCATTTTTG",
            DSCR8 = "GGCATGTTCTAAATGGCAGCTC",
            DSCR8 = "CCAGGCTCCTTCATTTTTGCTC",
            DSCR8 = "GGTCCAGGCTCCTTCATTTTTG")
res <- testPrimer(forward,reverse)

library(lucky)
forward = c(FASN = "ACAGCGGGGAATGGGTACT",
            SCD = "TCATAATTCCCGACGTGGCT",
            PPARG = "GGGATCAGCTCCGTGGATCT",
            ACACA = "TCACACCTGAAGACCTTAAAGCC",
            ACTB = "CATGTACGTTGCTATCCAGGC",
            TNF = "TGGCGTGGAGCTGAGAGATA",
            IL6 = "GAGTAGTGAGGAACAAGCCAGA",
            PCK1 = "AAGGTGGGGACGTTCAGAATC",
            G6PC = "CACTTCCGTGCCCCTGATAA")
reverse = c(FASN = "GACTGGTACAACGAGCGGAT",
            SCD = "CCCAGAAATACCAGGGCACA",
            PPARG = "TGCACTTTGGTACTCTTGAAGTT",
            ACACA = "AGCCCACACTGCTTGTACTG",
            ACTB = "CTCCTTAATGTCACGCACGAT",
            TNF = "TGATGGCAGAGAGGAGGTTG",
            IL6 = "AAGCTGCGCAGAATGAGATGA",
            PCK1 = "ATGGTTCCCTGCCTCATTCC",
            G6PC = "TAGTATACACCTGCTGTGCCC")
res <- testPrimer(forward,reverse)

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.