Correct load data for Run mmod #15
Description
Dear team mmod:
I can check that different libraries for load data to genind object can alter results of mmod functions
I am used adegenet library for previous analysis and create a DNAbin object.
obj_4 <- fasta2DNAbin("/media/737_alp_llam_end.fa", chunk=10)
Converting FASTA alignment into a DNAbin object...
Finding the size of a single genome...
genome size is: 468 nucleotides
( 2 lines per genome )
Importing sequences...
Forming final object...
...done.
obj_4
737 DNA sequences in binary format stored in a matrix.
All sequences of same length: 468
Labels:
B2-A135
E1-A130
F1-A131
B10-A235
B9-A216
C2-A136
...
Base composition:
a c g t
0.283 0.283 0.164 0.271
(Total: 344.92 kb)
Adegenet library have a function to pass DNAbin object to genind object. And Give these result 28 Loci
adegent_library <- DNAbin2genind(obj_4, pop = Pop)
/// GENIND OBJECT /////////
// 737 individuals; 28 loci; 58 alleles; size: 238.4 Kb
// Basic content
@tab: 737 x 58 matrix of allele counts
@loc.n.all: number of alleles per locus (range: 2-3)
@loc.fac: locus factor for the 58 columns of @tab
@all.names: list of allele names for each locus
@ploidy: ploidy of each individual (range: 1-1)
@type: codom
@call: DNAbin2genind(x = obj_4, pop = Pop)
// Optional content
@pop: population of each individual (group size range: 48-314)
But using convert function of mmod these give me 1 locus
mmod_library <- as.genind.DNAbin(obj_4, pop = Pop)
/// GENIND OBJECT /////////
// 737 individuals; 1 locus; 57 alleles; size: 228.3 Kb
// Basic content
@tab: 737 x 57 matrix of allele counts
@loc.n.all: number of alleles per locus (range: 57-57)
@loc.fac: locus factor for the 57 columns of @tab
@all.names: list of allele names for each locus
@ploidy: ploidy of each individual (range: 1-1)
@type: codom
@call: .local(.Object = .Object, tab = ..1, pop = ..2, ploidy = 1)
// Optional content
@pop: population of each individual (group size range: 48-314)
If I run Phi_st_Meirmans function of mmod the results are differents
Phi_st_Meirmans(adegent_library)
$per.locus
6 15 19 30 31 32 34 35 36 38
-1.9153758 -2.1545447 -1.9942762 -26.8815757 -1.9547215 8.6540814 -0.8085354 73.8280912 47.8747794 -0.6461673
39 55 59 61 67 69 73 91 126 192
-0.6579821 -1.8710735 -1.9347715 -1.9347715 8.7029927 -2.0180501 -1.9347715 -0.5389611 7.0012439 -1.2773257
212 218 219 230 231 259 271 284
6.1651727 -2.9712335 -2.9370603 9.4423593 -1.9347715 -3.1745577 -14.9206610 7.8309535
$global
[1] 29.40818
Phi_st_Meirmans(mmod_library)
$per.locus
L1
0.8883799
$global
[1] 0.8883799
I apreciated your feed back,
PD: For my research actually I am using the as.genind.DNAbin function for run mmod.