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<h2 id="Julia-version">Julia version<a class="anchor-link" href="#Julia-version">¶</a></h2><p>Current code supports Julia version 1.0 and 0.7. For reproducibility, listing the machine information below:</p>
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<h2 id="Installation-instructions">Installation instructions<a class="anchor-link" href="#Installation-instructions">¶</a></h2><p><code>MendelKinship</code> currently supports Julia version 1.0 and 1.1, but it is currently an unregistered package. To install, press <code>]</code> to invoke the package manager mode and install these packages by typing:</p>
<h2 id="Data-used-in-Examples">Data used in Examples<a class="anchor-link" href="#Data-used-in-Examples">¶</a></h2><p>The input for all examples in this tutorial can be obtained from the free application <a href="http://www.genetics.ucla.edu/software/mendel">Mendel v16</a> option 29a. These data were obtained from the 1000 genome project, containing 85 people and 253141 SNPs, half of which have $maf< 0.05$. Using these founders' genotype, we simulated 127 extra people, resulting in 27 pedigrees and 212 people. Although the 85 individuals are treated as founders, they were actually somewhat related, and this is reflected in the kinship comparison in the 2nd example below. For more information on this dataset, please see Mendel's documentation example 29.4.</p>
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<h2 id="Data-used-in-Examples">Data used in Examples<a class="anchor-link" href="#Data-used-in-Examples">¶</a></h2><p>The input for all examples in this tutorial can be obtained from the free application <a href="http://software.genetics.ucla.edu/download?package=1">Mendel v16</a> option 29a. These data were obtained from the 1000 genome project, containing 85 people and 253141 SNPs, half of which have maf$< 0.05$. Using these founders' genotype, we simulated 127 extra people, resulting in 27 pedigrees and 212 people. Although the 85 individuals are treated as founders, they were actually somewhat related, and this is reflected in the kinship comparison in the 2nd example below. For more information on this dataset, please see Mendel's documentation example 29.4.</p>
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<h2 id="Using-PLINK-compressed-file-as-input">Using PLINK compressed file as input<a class="anchor-link" href="#Using-PLINK-compressed-file-as-input">¶</a></h2><p>MendelKinship additionally accepts <a href="https://www.cog-genomics.org/plink2/formats#bed">PLINK binary format</a> as input, in which case the triplets (<code>data.bim</code>, <code>data.bed</code>, <code>data.fam</code>) must all be present. In this tutorial, there are no examples that uses these to import pedigree and SNP information. But if available, one can import the data by specifying the following in the control file:</p>
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<p><code>plink_input_basename = data</code></p>
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<p>However, sometimes the .fam file contains non-unique person id (2nd column of .fam file) across different pedigrees, which is currently <strong>not</strong> permitted. A person's id cannot be repeated in other pedigrees, even if it is contextually clear that they are different persons. This will be fixed in the near future.</p>
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<p>However, sometimes the .fam file contains non-unique person id (2nd column of .fam file) across different pedigrees, which is currently <strong>not</strong> permitted in MendelKinship. A person's id cannot be repeated in other pedigrees, even if it is contextually clear that they are different persons. This will be fixed in the near future.</p>
<pre>┌ Info: Recompiling stale cache file /Users/biona001/.julia/compiled/v1.0/MendelKinship/jENRZ.ji for MendelKinship [57586ee1-7d7e-549d-a2d8-59dc17d6b397]
<h2 id="Conclusions">Conclusions<a class="anchor-link" href="#Conclusions">¶</a></h2><p>MendelKinship provides a rapid way to calculate the theoretical kinship, which requires accurate pedigrees, and the empirical kinships, which requires genotypes at multiple markers. Further, it can compare these kinships when both the pedigrees and markers are available.</p>
"`MendelKinship` currently supports Julia version 1.0, but it an unregistered package. To install, press `]` to enter the package manager mode and install the following packages:\n",
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"`MendelKinship` currently supports Julia version 1.0 and 1.1, but it is currently an unregistered package. To install, press `]` to invoke the package manager mode and install these packages by typing:\n",
"For reproducibility, listing the machine information below:"
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"cell_type": "markdown",
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"\n",
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"## When to use MendelKinship\n",
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"`MendelKinship.jl` is capable of calculating the theoretical kinship coefficient $\\Phi_{ij}$ as long as a [valid pedigree structure](https://openmendel.github.io/MendelBase.jl/#pedigree-file) is provided. When SNP markers are available, `MendelKinship.jl` can also calculate empirical kinship coefficients using GRM, robust GRM, or Method of Moments methods (see [this paper](https://onlinelibrary.wiley.com/doi/abs/10.1002/gepi.20584) and [this paper](https://academic.oup.com/bioinformatics/article/26/22/2867/228512) for details). Here we recommend the Robust GRM or MoM (default) method because their estimates are more robust in the presence of rare alleles. \n",
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"## Data used in Examples\n",
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"The input for all examples in this tutorial can be obtained from the free application [Mendel v16](http://www.genetics.ucla.edu/software/mendel) option 29a. These data were obtained from the 1000 genome project, containing 85 people and 253141 SNPs, half of which have $maf< 0.05$. Using these founders' genotype, we simulated 127 extra people, resulting in 27 pedigrees and 212 people. Although the 85 individuals are treated as founders, they were actually somewhat related, and this is reflected in the kinship comparison in the 2nd example below. For more information on this dataset, please see Mendel's documentation example 29.4. "
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"The input for all examples in this tutorial can be obtained from the free application [Mendel v16](http://software.genetics.ucla.edu/download?package=1) option 29a. These data were obtained from the 1000 genome project, containing 85 people and 253141 SNPs, half of which have maf$< 0.05$. Using these founders' genotype, we simulated 127 extra people, resulting in 27 pedigrees and 212 people. Although the 85 individuals are treated as founders, they were actually somewhat related, and this is reflected in the kinship comparison in the 2nd example below. For more information on this dataset, please see Mendel's documentation example 29.4. "
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"`plink_input_basename = data` \n",
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"However, sometimes the .fam file contains non-unique person id (2nd column of .fam file) across different pedigrees, which is currently **not** permitted. A person's id cannot be repeated in other pedigrees, even if it is contextually clear that they are different persons. This will be fixed in the near future."
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"However, sometimes the .fam file contains non-unique person id (2nd column of .fam file) across different pedigrees, which is currently **not** permitted in MendelKinship. A person's id cannot be repeated in other pedigrees, even if it is contextually clear that they are different persons. This will be fixed in the near future."
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"┌ Info: Recompiling stale cache file /Users/biona001/.julia/compiled/v1.0/MendelKinship/jENRZ.ji for MendelKinship [57586ee1-7d7e-549d-a2d8-59dc17d6b397]\n",
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"└ @ Base loading.jl:1190\n"
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"Reading the data.\n",
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"The current working directory is \"/Users/biona001/.julia/dev/MendelKinship/test/kinship_tutorial\".\n",
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"The current working directory is \"/Users/biona001/Benjamin_Folder/UCLA/research/open mendel related/Tutorials/Kinship\".\n",
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"The current working directory is \"/Users/biona001/.julia/dev/MendelKinship/test/kinship_tutorial\".\n",
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"The current working directory is \"/Users/biona001/Benjamin_Folder/UCLA/research/open mendel related/Tutorials/Kinship\".\n",
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"## Conclusions\n",
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"MendelKinship provides a rapid way to calculate the theoretical kinship, which requires accurate pedigrees, and the empirical kinships, which requires genotypes at multiple markers. Further, it can compare these kinships when both the pedigrees and markers are available. "
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