test_findgRNAsSpCas9 <- function()
{
featureWeightMatrixFile <- system.file("extdata", "Morenos-Mateo.csv",
package = "CRISPRseek")
gRNAs <- findgRNAs(inputFilePath = system.file("extdata",
"cpf1.fa", package = "CRISPRseek"),
findPairedgRNAOnly=FALSE,
pairOutputFile = "testpairedgRNAs-SpCas9.xls",
PAM="NGG", PAM.location = "3prime", PAM.size = 3,
overlap.gRNA.positions = c(17, 18),
baseBeforegRNA = 4, baseAfterPAM = 3,
calculategRNAEfficacy= TRUE,
rule.set = "CRISPRscan",
featureWeightMatrixFile = featureWeightMatrixFile,
efficacyFile = "testCRISPRscanEfficacy.xls")
gRNAs_truth <- readRDS(system.file("extdata",
"gRNAsSpCas9.RDS", package = "CRISPRseek"))
checkEquals(gRNAs, gRNAs_truth)
effi_truth <- readRDS( system.file("extdata",
"CRISPRscanEff.RDS", package = "CRISPRseek"))
effi <- read.table("testCRISPRscanEfficacy.xls", sep = "\t", header = TRUE)
checkEquals(effi, effi_truth)
}
test_findgRNAsCpf1 <- function()
{
gRNAs <- findgRNAs(inputFilePath = system.file("extdata",
"cpf1.fa", package = "CRISPRseek"),
findPairedgRNAOnly=FALSE,
pairOutputFile = "testpairedgRNAs-cpf1.xls",
PAM="TTTN", PAM.location = "5prime", PAM.size = 4,
overlap.gRNA.positions = c(19,23),
baseBeforegRNA = 8, baseAfterPAM = 26,
calculategRNAEfficacy= TRUE,
rule.set = "DeepCpf1",
efficacyFile = "testcpf1Efficacy.xls")
gRNAs_truth <- readRDS(system.file("extdata",
"gRNAsCpf1.RDS", package = "CRISPRseek"))
checkEquals(gRNAs, gRNAs_truth)
effi_truth <- readRDS( system.file("extdata",
"Cpf1Eff.RDS", package = "CRISPRseek"))
effi <- read.table("testcpf1Efficacy.xls", sep = "\t", header = TRUE)
checkEquals(effi, effi_truth)
}
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