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HapSim specifications


Unique identifier OMICS_08661
Name HapSim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Giovanni Montana

Publication for HapSim

HapSim citations


Selection of X chromosome Inactivation Model

Cancer Inform
PMCID: 5751921
PMID: 29308008
DOI: 10.1177/1176935117747272

[…] were in high linkage disequilibrium (ld) with the causal variant for the disease of interest, which we denoted as snp1 and snp2. to generate the genotypes for snps in ld, we employed the r package “hapsim,” which is a simulation tool for generating haplotype data based on minor allele frequency (maf) and ld coefficients., specifically, hapsim generates haplotypes for each of the 2 strands […]


Do little interactions get lost in dark random forests?

BMC Bioinformatics
PMCID: 4815164
PMID: 27029549
DOI: 10.1186/s12859-016-0995-8

[…] snps was d′=0.69 (sd 0.35) and the correlation r2=0.14 (sd 0.23). for each simulated dataset, 100 snps were randomly selected out of these region, and new data with ld structure was simulated using hapsim []. effects of βm=βi=0 and all combinations of βm=(0.4,0.8) and βi=(0.4,0.8) were simulated., on each dataset, random forests with 500 trees each were grown with a varying number of snps […]


Data Simulation in Machine Olfaction with the R Package Chemosensors

PLoS One
PMCID: 3935855
PMID: 24586410
DOI: 10.1371/journal.pone.0088839

[…] the distribution of data sets and software for data generation. published packages for data simulation include the fwsim package for functional magnetic resonance imaging , the packages ibdsim and hapsim in statistical genetics , and the simframe package for building a general-purpose framework for statistical simulations ., our manuscript is organized as follows. we begin with a description […]


Blocking Approach for Identification of Rare Variants in Family Based Association Studies

PLoS One
PMCID: 3900483
PMID: 24465912
DOI: 10.1371/journal.pone.0086126

[…] schemes with blocks, as it preserves the independence assumption across blocks. haplotypes for unrelated founders with desired maf and ld structure are simulated using the same procedure as in hapsim , then we passed down the haplotypes to the remaining individuals assuming no recombination. for each set of genotypes, the binary disease status for each individual was simulated using […]


Computationally efficient permutation based confidence interval estimation for tail area FDR

Front Genet
PMCID: 3775454
PMID: 24062767
DOI: 10.3389/fgene.2013.00179

[…] methods under a different set of realistic genomic testing conditions, snps and gaussian traits were simulated with dependencies and then tested for associations using linear additive models. the hapsim (montana, ) r package was used to randomly generate haplotypes corresponding to specified ranges of ld, from which the snp data was constructed. allele frequencies were sampled from a uniform […]


A Linkage Disequilibrium–Based Approach to Selecting Disease Associated Rare Variants

PLoS One
PMCID: 3708889
PMID: 23874919
DOI: 10.1371/journal.pone.0069226

[…] region. however, two of the variants were not polymorphic and so we removed them from further consideration. the pairwise ld pattern () and the maf information were downloaded from the database. hapsim is a simulation tool for generating haplotype data with pre-specified allele frequencies and ld coefficients. we used hapsim to generate haplotypes for each of the two strands of the dna […]

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HapSim institution(s)
Department of Mathematics, Imperial College London, UK

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