barchart: Bar plot representation of an snmf Q-matrix
In LEA: LEA: an R package for Landscape and Ecological Association Studies
Description
Usage
Arguments
Value
Author(s)
See Also
Examples
Description
This function displays a bar plot/bar chart representation of the Q-matrix computed from an snmf run. The function can use a sort by Q option. See snmf.
Usage
1
Arguments
object
an snmfProject object.
K
an integer value corresponding to number of ancestral populations.
run
an integer value. Usually the run number that minimizes the cross-entropy criterion.
sort.by.Q
a Boolean value indicating whether individuals should be sorted by their
ancestry or not.
lab
a list of individual labels.
...
other parameters of the function barplot.default.
Value
A permutation of individual labels used in the sort.by.Q option (order). Displays the
Q matrix.
Author(s)
Olivier Francois
See Also
Examples
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# creation of a genotype file: genotypes.geno.
# 400 SNPs for 50 individuals.
data("tutorial")
write.geno(tutorial.R, "genotypes.geno")
################
# running snmf #
################
project.snmf <- snmf("genotypes.geno",
K = 4, entropy = TRUE,
repetitions = 10,
project = "new")
# get the cross-entropy value for each run
ce <- cross.entropy(project.snmf, K = 4)
# select the run with the lowest cross-entropy value
best <- which.min(ce)
# plot the ancestry coefficients for the best run and K = 4
my.colors <- c("tomato", "lightblue", "olivedrab", "gold")
barchart(project.snmf, K = 4, run = best,
border = NA, space = 0, col = my.colors,
xlab = "Individuals", ylab = "Ancestry proportions",
main = "Ancestry matrix") -> bp
axis(1, at = 1:length(bp$order),
labels = bp$order, las = 3,
cex.axis = .4)
Example output
[1] "genotypes.geno"
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 958371504
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 958371504
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94597613065904
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[====================================]
Number of iterations: 96
Least-square error: 5468.100416
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453066
Cross-Entropy (masked data): 0.559319
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1740012072
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1740012072
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94598394706472
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========================]
Number of iterations: 66
Least-square error: 5477.041325
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453226
Cross-Entropy (masked data): 0.587829
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1334902936
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1334902936
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94597989597336
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[================]
Number of iterations: 44
Least-square error: 5437.926383
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.450695
Cross-Entropy (masked data): 0.630775
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1773032917
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1773032917
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 4607182420573050325
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================================]
Number of iterations: 89
Least-square error: 5457.888087
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453561
Cross-Entropy (masked data): 0.551309
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 542953344
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 542953344
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94597197647744
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========================]
Number of iterations: 67
Least-square error: 5448.288169
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.451827
Cross-Entropy (masked data): 0.666003
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1937802772
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1937802772
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 4547005792867354132
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 41
Least-square error: 5479.404372
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.455871
Cross-Entropy (masked data): 0.589988
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1493151524
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1493151524
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1493151524
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================]
Number of iterations: 61
Least-square error: 5476.770321
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.452084
Cross-Entropy (masked data): 0.60964
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1128439139
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1128439139
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1128439139
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================================]
Number of iterations: 93
Least-square error: 5457.741656
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.451802
Cross-Entropy (masked data): 0.61466
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 634541841
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 634541841
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 4929509137
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================================]
Number of iterations: 90
Least-square error: 5454.829740
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.452119
Cross-Entropy (masked data): 0.569406
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 743103390
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 743103390
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 743103390
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================]
Number of iterations: 103
Least-square error: 5478.247801
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.454737
Cross-Entropy (masked data): 0.53056
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
LEA documentation built on Nov. 8, 2020, 8:19 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value Author(s) See Also Examples
Description
This function displays a bar plot/bar chart representation of the Q-matrix computed from an snmf run. The function can use a sort by Q option. See snmf.
Usage
1 |
Arguments
object |
an snmfProject object. |
K |
an integer value corresponding to number of ancestral populations. |
run |
an integer value. Usually the run number that minimizes the cross-entropy criterion. |
sort.by.Q |
a Boolean value indicating whether individuals should be sorted by their ancestry or not. |
lab |
a list of individual labels. |
... |
other parameters of the function |
Value
A permutation of individual labels used in the sort.by.Q option (order). Displays the Q matrix.
Author(s)
Olivier Francois
See Also
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | # creation of a genotype file: genotypes.geno.
# 400 SNPs for 50 individuals.
data("tutorial")
write.geno(tutorial.R, "genotypes.geno")
################
# running snmf #
################
project.snmf <- snmf("genotypes.geno",
K = 4, entropy = TRUE,
repetitions = 10,
project = "new")
# get the cross-entropy value for each run
ce <- cross.entropy(project.snmf, K = 4)
# select the run with the lowest cross-entropy value
best <- which.min(ce)
# plot the ancestry coefficients for the best run and K = 4
my.colors <- c("tomato", "lightblue", "olivedrab", "gold")
barchart(project.snmf, K = 4, run = best,
border = NA, space = 0, col = my.colors,
xlab = "Individuals", ylab = "Ancestry proportions",
main = "Ancestry matrix") -> bp
axis(1, at = 1:length(bp$order),
labels = bp$order, las = 3,
cex.axis = .4)
|
Example output
[1] "genotypes.geno"
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 958371504
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 958371504
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 1 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94597613065904
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[====================================]
Number of iterations: 96
Least-square error: 5468.100416
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run1/genotypes_r1.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453066
Cross-Entropy (masked data): 0.559319
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1740012072
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1740012072
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 2 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94598394706472
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========================]
Number of iterations: 66
Least-square error: 5477.041325
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run2/genotypes_r2.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453226
Cross-Entropy (masked data): 0.587829
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1334902936
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1334902936
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 3 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94597989597336
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[================]
Number of iterations: 44
Least-square error: 5437.926383
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run3/genotypes_r3.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.450695
Cross-Entropy (masked data): 0.630775
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1773032917
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1773032917
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 4 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 4607182420573050325
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=================================]
Number of iterations: 89
Least-square error: 5457.888087
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run4/genotypes_r4.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.453561
Cross-Entropy (masked data): 0.551309
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 542953344
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 542953344
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 5 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 94597197647744
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=========================]
Number of iterations: 67
Least-square error: 5448.288169
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run5/genotypes_r5.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.451827
Cross-Entropy (masked data): 0.666003
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1937802772
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1937802772
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 6 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 4547005792867354132
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===============]
Number of iterations: 41
Least-square error: 5479.404372
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run6/genotypes_r6.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.455871
Cross-Entropy (masked data): 0.589988
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1493151524
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1493151524
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 7 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1493151524
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================]
Number of iterations: 61
Least-square error: 5476.770321
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run7/genotypes_r7.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.452084
Cross-Entropy (masked data): 0.60964
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 1128439139
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 1128439139
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 8 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 1128439139
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[===================================]
Number of iterations: 93
Least-square error: 5457.741656
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run8/genotypes_r8.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.451802
Cross-Entropy (masked data): 0.61466
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 634541841
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 634541841
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 9 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 4929509137
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[==================================]
Number of iterations: 90
Least-square error: 5454.829740
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run9/genotypes_r9.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.452119
Cross-Entropy (masked data): 0.569406
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
[1] 743103390
[1] "*************************************"
[1] "* create.dataset *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-s (seed random init) 743103390
-r (percentage of masked data) 0.05
-x (genotype file in .geno format) /work/tmp/genotypes.geno
-o (output file in .geno format) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
Write genotype file with masked data, /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
[1] "*************************************"
[1] "* sNMF K = 4 repetition 10 *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (input file) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
-q (individual admixture file) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.Q
-g (ancestral frequencies file) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.G
-i (number max of iterations) 200
-a (regularization parameter) 10
-s (seed random init) 743103390
-e (tolerance error) 1E-05
-p (number of processes) 1
- diploid
Read genotype file /work/tmp/genotypes.snmf/masked/genotypes_I.geno: OK.
Main algorithm:
[ ]
[=======================================]
Number of iterations: 103
Least-square error: 5478.247801
Write individual ancestry coefficient file /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.Q: OK.
Write ancestral allele frequency coefficient file /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.G: OK.
[1] "*************************************"
[1] "* cross-entropy estimation *"
[1] "*************************************"
summary of the options:
-n (number of individuals) 50
-L (number of loci) 400
-K (number of ancestral pops) 4
-x (genotype file) /work/tmp/genotypes.geno
-q (individual admixture) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.Q
-g (ancestral frequencies) /work/tmp/genotypes.snmf/K4/run10/genotypes_r10.4.G
-i (with masked genotypes) /work/tmp/genotypes.snmf/masked/genotypes_I.geno
- diploid
Cross-Entropy (all data): 0.454737
Cross-Entropy (masked data): 0.53056
The project is saved into :
genotypes.snmfProject
To load the project, use:
project = load.snmfProject("genotypes.snmfProject")
To remove the project, use:
remove.snmfProject("genotypes.snmfProject")
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