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

In huangwb8/luckyExperiment: useful functions for biology experiment

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

Description

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

Usage

testPrimer(
  forward,
  reverse,
  species = "human",
  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
species	one of "human" or "mouse"
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)

huangwb8/luckyExperiment documentation built on June 29, 2023, 10:15 a.m.