sequence.simulation.seqgen: Simulate sequence data of individuals in the transmissiion...
In wdelva/RSimpactHelp: Pre- and Post-simulation helper functions for RSimpact Cyan

View source: R/sequence.simulation.seqgen.R

Simulate sequence data of individuals in the transmissiion network using seq-gen tool

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sequence.simulation.seqgen(dir.seq = dir, seq.gen.tool = "seq-gen",
  datalist = datalist, seeds.num = 123, endpoint = 40,
  limitTransmEvents = 3, hiv.seq.file = "hiv.seq.C.pol.j.fasta")

`dir.seq`	Directory where seq-gen tool is stored, sequences data may also be stored there
`seq.gen.tool`	Name of the file for compiled seq-gen
`datalist`	The datalist that is produced by `readthedata()`
`seeds.num`	Seed number for reproducability
`endpoint`	Only transmission events that took place before this point in simulation time
`limitTransmEvents`	Minimum number of individuals in that transmission network (one transmission network per HIV seeding individual)
`hiv.seq.file`	File containing seed HIV sequences in FASTA format, it might be in same repository as seq-gen