{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# `natsel_timehet` -- a test of branch heterogeneity\n", "\n", "We employ codon models to test whether the mode of natural selection affecting human and chimpanzee lineages is distinctive. This is done by specifying the edges of interest ([Yang 1998](https://www.ncbi.nlm.nih.gov/pubmed/9580986)). (Note I'm setting `optimise_motif_probs=False` to speed up execution of the examples, not because it's a good idea!)" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
Statistics
LRdfpvalue
4.924810.0265
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
hypothesiskeylnLnfpDLCunique_Q
null'GNC-null'-6713.273323True
alt'GNC-alt'-6710.810924True
\n" ], "text/plain": [ "Statistics\n", "======================\n", " LR df pvalue\n", "----------------------\n", "4.9248 1 0.0265\n", "----------------------\n", "=================================================================\n", "hypothesis key lnL nfp DLC unique_Q\n", "-----------------------------------------------------------------\n", " null 'GNC-null' -6713.2733 23 True \n", " alt 'GNC-alt' -6710.8109 24 True \n", "-----------------------------------------------------------------" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from cogent3.app import io, evo\n", "\n", "loader = io.load_aligned(format=\"fasta\", moltype=\"dna\")\n", "aln = loader(\"../data/primate_brca1.fasta\")\n", "\n", "hc_differ = evo.natsel_timehet(\"GNC\",\n", " tree=\"../data/primate_brca1.tree\",\n", " optimise_motif_probs=False,\n", " tip1=\"Human\", tip2=\"Chimpanzee\")\n", "result = hc_differ(aln)\n", "result" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "

GNC-alt

\n", "

log-likelihood = -6710.8109

\n", "

number of free parameters = 24

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Global params
A>CA>GA>TC>AC>GC>TG>AG>CG>TT>A
0.86203.53610.97901.66982.20596.26307.92091.22650.80241.2882
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T>C
3.0675
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
Edge params
edgeparentlengthomega
Galagoroot0.52370.7906
HowlerMonroot0.13390.7906
Rhesusedge.30.06400.7906
Orangutanedge.20.02330.7906
Gorillaedge.10.00750.7906
Humanedge.00.01822.6351
Chimpanzeeedge.00.00852.6351
edge.0edge.10.00000.7906
edge.1edge.20.01000.7906
edge.2edge.30.03660.7906
edge.3root0.02380.7906
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Motif params
AAAAACAAGAATACAACCACGACTAGAAGC
0.05560.02350.03440.05560.02280.00460.00080.02890.02310.0286
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AGGAGTATAATCATGATTCAACACCAGCAT
0.01400.03810.01860.00700.01280.01920.01960.00520.02380.0221
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
CCACCCCCGCCTCGACGCCGGCGTCTACTC
0.01950.00620.00060.02630.00110.00090.00230.00320.01370.0078
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
CTGCTTGAAGACGAGGATGCAGCCGCGGCT
0.01250.01050.07550.01050.03030.03150.01580.00960.00140.0137
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
GGAGGCGGGGGTGTAGTCGTGGTTTACTAT
0.01610.00900.00670.01330.01480.00700.00690.02130.00230.0101
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
TCATCCTCGTCTTGCTGGTGTTTATTCTTG
0.02210.00820.00150.02510.00180.00400.02010.02120.00780.0108
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
TTT
0.0187
\n" ], "text/plain": [ "GNC-alt\n", "log-likelihood = -6710.8109\n", "number of free parameters = 24\n", "============================================================================\n", " A>C A>G A>T C>A C>G C>T G>A G>C\n", "----------------------------------------------------------------------------\n", "0.8620 3.5361 0.9790 1.6698 2.2059 6.2630 7.9209 1.2265\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "==========================\n", " G>T T>A T>C\n", "--------------------------\n", "0.8024 1.2882 3.0675\n", "--------------------------\n", "\n", "========================================\n", " edge parent length omega\n", "----------------------------------------\n", " Galago root 0.5237 0.7906\n", " HowlerMon root 0.1339 0.7906\n", " Rhesus edge.3 0.0640 0.7906\n", " Orangutan edge.2 0.0233 0.7906\n", " Gorilla edge.1 0.0075 0.7906\n", " Human edge.0 0.0182 2.6351\n", "Chimpanzee edge.0 0.0085 2.6351\n", " edge.0 edge.1 0.0000 0.7906\n", " edge.1 edge.2 0.0100 0.7906\n", " edge.2 edge.3 0.0366 0.7906\n", " edge.3 root 0.0238 0.7906\n", "----------------------------------------\n", "============================================================================\n", " AAA AAC AAG AAT ACA ACC ACG ACT\n", "----------------------------------------------------------------------------\n", "0.0556 0.0235 0.0344 0.0556 0.0228 0.0046 0.0008 0.0289\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "============================================================================\n", " AGA AGC AGG AGT ATA ATC ATG ATT\n", "----------------------------------------------------------------------------\n", "0.0231 0.0286 0.0140 0.0381 0.0186 0.0070 0.0128 0.0192\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "============================================================================\n", " CAA CAC CAG CAT CCA CCC CCG CCT\n", "----------------------------------------------------------------------------\n", "0.0196 0.0052 0.0238 0.0221 0.0195 0.0062 0.0006 0.0263\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "============================================================================\n", " CGA CGC CGG CGT CTA CTC CTG CTT\n", "----------------------------------------------------------------------------\n", "0.0011 0.0009 0.0023 0.0032 0.0137 0.0078 0.0125 0.0105\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "============================================================================\n", " GAA GAC GAG GAT GCA GCC GCG GCT\n", "----------------------------------------------------------------------------\n", "0.0755 0.0105 0.0303 0.0315 0.0158 0.0096 0.0014 0.0137\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "============================================================================\n", " GGA GGC GGG GGT GTA GTC GTG GTT\n", "----------------------------------------------------------------------------\n", "0.0161 0.0090 0.0067 0.0133 0.0148 0.0070 0.0069 0.0213\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "============================================================================\n", " TAC TAT TCA TCC TCG TCT TGC TGG\n", "----------------------------------------------------------------------------\n", "0.0023 0.0101 0.0221 0.0082 0.0015 0.0251 0.0018 0.0040\n", "----------------------------------------------------------------------------\n", "\n", "continued: \n", "==============================================\n", " TGT TTA TTC TTG TTT\n", "----------------------------------------------\n", "0.0201 0.0212 0.0078 0.0108 0.0187\n", "----------------------------------------------" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "result.alt.lf" ] } ], "metadata": { "kernelspec": { "display_name": "Python [conda env:c3dev] *", "language": "python", "name": "conda-env-c3dev-py" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.1" }, "widgets": { "application/vnd.jupyter.widget-state+json": { "state": {}, "version_major": 2, "version_minor": 0 } } }, "nbformat": 4, "nbformat_minor": 4 }