[R-sig-genetics] ape, read.dna to phase fasta file not working properly, tajima

[Ella Bowles]

​
 fasta8c18.fa
<https://drive.google.com/file/d/0B6qb8IlaQGFZX0Q0YzNUVGNHV1E/view?usp=drive_web>
​Hello,

I'm trying to complete the very simple task of reading in an unphased fasta
file and phasing it using ape, and then calculating Tajima's D using pegas,
but my data doesn't seem to be reading in correctly. Input and output is as
follows:
library("ape")
library("adegenet")
library("ade4")
library("pegas")

> DNAbin8c18 <- read.dna(file="fasta8c18.fa", format="f")
> data(DNAbin8c18)
Warning message:
In data(DNAbin8c18) : data set ‘DNAbin8c18’ not found

##clearly the data is not read in properly, so looked at what had been
loaded

> DNAbin8c18
817452 DNA sequences in binary format stored in a matrix.

All sequences of same length: 96

Labels:
CLocus_12706_Sample_1_Locus_34105_Allele_0 [BayOfIslands_s08...
CLocus_12706_Sample_2_Locus_31118_Allele_0 [BayOfIslands_s08...
CLocus_12706_Sample_3_Locus_30313_Allele_0 [BayOfIslands_s09...
CLocus_12706_Sample_5_Locus_33345_Allele_0 [BayOfIslands_s09...
CLocus_12706_Sample_7_Locus_37388_Allele_0 [BayOfIslands_s09...
CLocus_12706_Sample_8_Locus_29451_Allele_0 [BayOfIslands_s09...
...

More than 10 million nucleotides: not printing base composition

##although likely won't work, trying taj d test to see what happens
> tajima.test(DNAbin8c18)
Error: cannot allocate vector of size 2489.3 Gb

​I'm sending the datafile along as a link as well.

Any thoughts would be much appreciated.

Ella​

-- 
Ella Bowles, PhD
Postdoctoral Researcher
Department of Biology
Concordia University

Website: https://ellabowlesphd.wordpress.com/
Email: bowlese at gmail.com

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