formatting dartR genlight data for sequoia?

[Peter Kriesner]

What would be a good way to go about formatting data from a dartR genlight object for subsequent relatedness analyses using the sequoia R package?

Cheers,

Peter K

[Jose Luis Mijangos]

Hi Peter,

Can you try the following code:

  library(dartR)

  library(sequoia)

  t1 <- platypus.gl

  t1 <- gl.filter.callrate(t1,threshold = 1)

  t1 <- gl.filter.monomorphs(t1)

  

  

  LifeHistData_2 <- as.data.frame(t1$ind.names)

  LifeHistData_2$Sex <- as.character(t1$other$ind.metrics$Sex)

  LifeHistData_2[LifeHistData_2=="F"] <- 1

  LifeHistData_2[LifeHistData_2=="M"] <- 2

  LifeHistData_2[LifeHistData_2==""] <- 3

  LifeHistData_2$Sex <- as.numeric(LifeHistData_2$Sex)

  

  LifeHistData_2$BirthYear <- as.character(t1$other$ind.metrics$AgeClass)

  LifeHistData_2[LifeHistData_2=="A"] <- 2000

  LifeHistData_2[LifeHistData_2=="J"] <- 2005

  LifeHistData_2$BirthYear <- as.numeric(LifeHistData_2$BirthYear)

  

  colnames(LifeHistData_2)<- c("ID","Sex","BirthYear")

  

  t_sequoia <- as.matrix(as.data.frame(t1))

  t_sequoia[is.na(t_sequoia)] <- "-9"

  t_sequoia_2 <- cbind(t1$ind.names,t_sequoia)

  t_sequoia_2 <- matrix(data=t_sequoia_2, ncol=ncol(t_sequoia)+1, nrow=nrow(t_sequoia))

  t_sequoia_2 <- as.data.frame(t_sequoia_2)

  GenoM <- GenoConvert(InFile=t_sequoia_2, InFormat="seq",Missing="-9",IDcol=1)

  

  GenoM_2 <- GenoM

  

  sequoia_res <- sequoia(GenoM = GenoM_2,Plot = F,UseAge = F,MaxSibshipSize=20)

  sequoia_res_2 <- GetMaybeRel(GenoM = GenoM_2,  LifeHistData =LifeHistData_2)

  

Cheers,

Luis