callPrimer3 {SPLINTER} | R Documentation |
call primer3 for a given set of DNAstringSet object
callPrimer3( seq, size_range = "150-500", Tm = c(57, 59, 62), name = "Primer1", primer3 = "primer3-2.3.7/bin/primer3_core", thermo.param = "primer3-2.3.7/src/primer3_config/", sequence_target = NULL, settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt" )
seq |
DNAstring object, one DNA string for the given amplicon |
size_range |
default: '151-500' |
Tm |
melting temprature parameters default:c(55,57,58) |
name |
name of the amplicon in chr_start_end format |
primer3 |
primer3 path |
thermo.param |
thermodynamic parameters folder |
sequence_target |
If one or more targets is specified then a legal primer pair must flank at least one of them. |
settings |
text file for parameters |
modified to include SEQUENCE_TARGET as an option
data.frame of designed primers and parameters
Altuna Akalin's modified Arnaud Krebs' original function further modified here by Diana Low
### NOT RUN ### # primer_results<-callPrimer3(seq='')