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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 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.