How to increase the number of primer set output in openPrimeR
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@marongiuluigi-7134
Last seen 3.2 years ago
European Union

I have generated a set of primers with openPrimeR, but I got only one set. How can I increase the number of sets returned byopenPrimeR, let's say to 10? Thanks

library("openPrimeR")
fasta.file <- system.file("extdata", "IMGT_data", "templates", 
                "Homo_sapiens_IGH_functional_exon.fasta", package = "openPrimeR")
# Load the template sequences from 'fasta.file'
seq.df.simple <- read_templates(fasta.file)
list.files(system.file("extdata", "settings", package = "openPrimeR"), pattern = "*\\.xml")
optimal.primers <- design_primers(template.df[1:2,], mode.directionality = "fw",
                                  settings = design.settings)
> sessionInfo( )
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] openPrimeR_1.12.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6              plyr_1.8.6              pillar_1.4.7            compiler_4.0.3         
 [5] RColorBrewer_1.1-2      GenomeInfoDb_1.26.2     XVector_0.30.0          bitops_1.0-6           
 [9] iterators_1.0.13        tools_4.0.3             zlibbioc_1.36.0         lifecycle_1.0.0        
[13] tibble_3.0.6            gtable_0.3.0            pkgconfig_2.0.3         rlang_0.4.10           
[17] foreach_1.5.1           rstudioapi_0.13         parallel_4.0.3          GenomeInfoDbData_1.2.4 
[21] stringr_1.4.0           dplyr_1.0.4             Biostrings_2.58.0       generics_0.1.0         
[25] S4Vectors_0.28.1        vctrs_0.3.6             IRanges_2.24.1          stats4_4.0.3           
[29] grid_4.0.3              tidyselect_1.1.0        glue_1.4.2              R6_2.5.0               
[33] reshape2_1.4.4          ggplot2_3.3.3           purrr_0.3.4             magrittr_2.0.1         
[37] scales_1.1.1            codetools_0.2-18        ellipsis_0.3.1          BiocGenerics_0.36.0    
[41] GenomicRanges_1.42.0    colorspace_2.0-0        stringi_1.5.3           lpSolveAPI_5.5.2.0-17.7
[45] RCurl_1.98-1.2          munsell_0.5.0           crayon_1.4.1
openPrimeR • 590 views
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openPrimeR will always only generate a single, optimal (find the minimal set of primers maximizing the coverage) primer set. If you want to create multiple primer sets, you can adjust the constraint settings.

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