[R-sig-genetics] genlight to treemix conversion

[Zhian Kamvar]

Hi Daniel,

I'm not exactly sure this will work, but this might help:

# Setting up fake data
library('adegenet')
x       <- glSim(100, 1e3, ploid=2)
pop(x)  <- rep(letters[1:5], each = 20)

# conversion 
altlist <- lapply(seppop(x), as.matrix)
get_pop_counts <- function(altmatrix){
  alt <- apply(altmatrix, 2, sum, na.rm = TRUE)
  ref <- apply(2 - altmatrix, 2, sum, na.rm = TRUE)
  paste(alt, ref, sep = ",")
}

dat <- data.frame(lapply(altlist, get_pop_counts))
write.table(dat, file = "mydata.treemix", sep = "\t", row.names = FALSE, col.names = TRUE)

Zhian
> On Mar 12, 2016, at 00:32 , Daniel Fulop <dfulop.ucd at gmail.com> wrote:
> 
> Dear all,
> 
> I’m wondering if someone has code for converting data from genlight to treemix format. If you do and wouldn’t mind sharing it I would be most grateful.
> 
> I think one could do as.matrix(genlight-object) and then sum the alleles for each population, but then I’m not sure how to deal with NAs.
> 
> Thanks!
> Dan.
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