prepare_primer_df | R Documentation |
Prepare a primer table for downstream analyses
prepare_primer_df( input_fasta, primer_length = 20, GCcheck = FALSE, GCmin = 0.4, GCmax = 0.6, GChalves = FALSE, GCsimilarity = 0.1 )
input_fasta |
A string. Name or filepath of the input FASTA file. |
primer_length |
A number. Sets the primer length. For applications involving two adjacent probes, the value should be set to two-fold the length of a single probe. |
GCcheck |
A logical. If TRUE, checks the GC contents of the primers and filters based on GCmin and GCmax. |
GCmin |
A decimal. If GCcheck is performed, this parameter determines the minimum proportional GC content. |
GCmax |
A decimal. If GCcheck is performed, this parameter determines the maximum proportional GC content. |
GChalves |
A logical. If TRUE, checks the GC contents separately for both halves of the primers and filters based on GCsimilarity. For example for applications involving two adjacent probes. |
GCsimilarity |
A number. If GChalves is performed, this parameter determines the maximum proportional GC content difference between the primer halves. |
A list containing sequence id conversions, primer matrix and a list of primers with their target sequences.
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