[adegenet-forum] Discrepancy in NA counts

[Biz Sheedy]

Dear All,

I am trying to read SNP data from Stacks into adegenet. I have tried
read.structure and read.genepop but they both give (the same) NA counts
that are higher than expected. Using read.table on the structure-formatted
file (with "ind" and "pop" inserted into the first two columns of row one)
gave the expected number of missing data.

I looked at a single population subset (both the original and the converted
data) in excel and found a locus where in the original data, all nine
individuals were "3", but in the converted data one individual was "NA".
The loci before and after this one both matched/were correct.

I am not sure what I have missed for this to happen, my R skills are
beginner at best. Any help with reading the data in correctly would be
greatly appreciated!

Thank you,
Elizabeth


R version 3.3.2
adegenet version 2.0.1

Data: 44 individuals, diploid, 4279 loci.

all<-read.structure("all_batch_1.stru", NA.char="0")

Total cells in excel: 376552
After read.structure/genepop: 44*8558=376552

0s in excel: 3952
0s after read.table; length(which(X==0)): 3952
NA after read.structure/genepop; sum(is.na(all$tab)): 4008
Difference: 56

Subset Chichi
Total cells: 77022
After read.structure/genepop: 9*8558=77022

0s in excel: 742
NA after read.structure/genepop; sum(is.na(chi$tab)): 756
Difference: 14



-- 
4-1-1 Amakubo
Department of Botany
National Museum of Nature and Science
Tsukuba, Ibaraki 305-0005
Japan

biz.sheedy at gmail.com
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