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| Title |
DHOEM: a statistical simulation software for simulating new markers in real SNP marker data
|
|---|---|
| Published in |
BMC Bioinformatics, December 2015
|
| DOI | 10.1186/s12859-015-0830-7 |
| Pubmed ID | |
| Authors |
Laval Jacquin, Tuong-Vi Cao, Cécile Grenier, Nourollah Ahmadi |
| Abstract |
Numerous simulation tools based on specific assumptions have been proposed to simulate populations. Here we present a simulation tool named DHOEM (densification of haplotypes by loess regression and maximum likelihood) which is free from population assumptions and simulates new markers in real SNP marker data. The main objective of DHOEM is to generate a new population, which incorporates real and simulated SNP by statistical learning from an initial population, which match the realized features of the latter. To demonstrate DHOEM's abilities, we used a sample of 704 haplotypes for 12 chromosomes with 8336 SNP from a synthetic population, used for breeding upland rice in Latin America. The distributions of allele frequencies, pairwise SNP LD coefficients and data structures, before and after marker densification of the associated marker data set, were shown to be in relatively good agreement at moderate degrees of marker densification. DHOEM is a user-friendly tool that allows the user to specify the level of marker density desired, with a user defined minor allele frequency (MAF) limit, which is produced in a reasonable computation time. DHOEM is a user-friendly and useful tool for simulation and methodological studies in quantitative genetics and breeding. |
X Demographics
The data shown below were collected from the profile of 1 X user who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Scientists | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 10 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Spain | 1 | 10% |
| France | 1 | 10% |
| Unknown | 8 | 80% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Postgraduate | 2 | 20% |
| Other | 1 | 10% |
| Student > Ph. D. Student | 1 | 10% |
| Student > Bachelor | 1 | 10% |
| Professor > Associate Professor | 1 | 10% |
| Other | 1 | 10% |
| Unknown | 3 | 30% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 4 | 40% |
| Computer Science | 2 | 20% |
| Biochemistry, Genetics and Molecular Biology | 1 | 10% |
| Unknown | 3 | 30% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 09 December 2015.
All research outputs
#20,298,249
of 22,835,198 outputs
Outputs from BMC Bioinformatics
#6,861
of 7,288 outputs
Outputs of similar age
#324,915
of 387,656 outputs
Outputs of similar age from BMC Bioinformatics
#143
of 149 outputs
Altmetric has tracked 22,835,198 research outputs across all sources so far. This one is in the 1st percentile – i.e., 1% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,288 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.4. This one is in the 1st percentile – i.e., 1% of its peers scored the same or lower than it.
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We're also able to compare this research output to 149 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.