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Merge remote-tracking branch 'origin' into dev/link-check-dan
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@mr8lu
mr8lu committed Nov 25, 2024
2 parents 23c6f66 + 252acea commit 7f14b3b
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207 changes: 24 additions & 183 deletions notebooks/GWAS/GWAS_coat_color.ipynb
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Original file line number Diff line number Diff line change
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"cell_type": "code",
"execution_count": null,
"id": "8ec900bd",
"metadata": {
"vscode": {
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"source": [
"%%bash\n",
Expand All @@ -75,11 +71,7 @@
"cell_type": "code",
"execution_count": null,
"id": "4d43ae73",
"metadata": {
"vscode": {
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"metadata": {},
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"source": [
"%%bash\n",
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"cell_type": "code",
"execution_count": null,
"id": "b3ba3eef",
"metadata": {
"vscode": {
"languageId": "r"
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},
"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
Expand All @@ -117,14 +105,7 @@
"cell_type": "code",
"execution_count": null,
"id": "ae20d01c",
"metadata": {
"gather": {
"logged": 1686580882939
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"vscode": {
"languageId": "r"
}
},
"metadata": {},
"outputs": [],
"source": [
"#add to your path\n",
Expand All @@ -136,11 +117,7 @@
"cell_type": "code",
"execution_count": null,
"id": "b219074a",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"metadata": {},
"outputs": [],
"source": [
"! mamba install -y -c bioconda plink vcftools"
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"cell_type": "code",
"execution_count": null,
"id": "e91c7a01",
"metadata": {
"gather": {
"logged": 1686579597925
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"vscode": {
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"metadata": {},
"outputs": [],
"source": [
"cd GWAS"
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"cell_type": "code",
"execution_count": null,
"id": "9b770f7f",
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"gather": {
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"metadata": {},
"outputs": [],
"source": [
"ls"
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"cell_type": "code",
"execution_count": null,
"id": "6570875d",
"metadata": {
"vscode": {
"languageId": "r"
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},
"metadata": {},
"outputs": [],
"source": [
"! vcftools --gzvcf pruned_coatColor_maf_geno.vcf.gz --plink --out coatColor"
Expand All @@ -215,14 +174,7 @@
"cell_type": "code",
"execution_count": null,
"id": "6c868a67",
"metadata": {
"gather": {
"logged": 1686581972147
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"vscode": {
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},
"metadata": {},
"outputs": [],
"source": [
"#unzip vcf\n",
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"cell_type": "code",
"execution_count": null,
"id": "8e11f991",
"metadata": {
"gather": {
"logged": 1686581979545
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"vscode": {
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"metadata": {},
"outputs": [],
"source": [
"#create list of minor alleles\n",
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"cell_type": "code",
"execution_count": null,
"id": "8cff47e3",
"metadata": {
"vscode": {
"languageId": "r"
}
},
"metadata": {},
"outputs": [],
"source": [
"! head minor_alleles"
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"cell_type": "code",
"execution_count": null,
"id": "dafa14a6",
"metadata": {
"gather": {
"logged": 1686582023237
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"vscode": {
"languageId": "r"
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},
"metadata": {},
"outputs": [],
"source": [
"#calculate missingness per locus\n",
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"cell_type": "code",
"execution_count": null,
"id": "5cf5f51b",
"metadata": {
"gather": {
"logged": 1686582030150
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"vscode": {
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},
"metadata": {},
"outputs": [],
"source": [
"#take a look at lmiss, which is the per locus rates of missingness\n",
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"cell_type": "code",
"execution_count": null,
"id": "915bb263",
"metadata": {
"gather": {
"logged": 1686582034753
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"vscode": {
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},
"metadata": {},
"outputs": [],
"source": [
"#peek at imiss which is the individual rates of missingness\n",
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"cell_type": "code",
"execution_count": null,
"id": "3b8f2d7f",
"metadata": {
"vscode": {
"languageId": "r"
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"metadata": {},
"outputs": [],
"source": [
"! plink --file coatColor --allow-no-sex --dog --make-bed --noweb --out coatColor.binary"
Expand All @@ -357,11 +273,7 @@
"cell_type": "code",
"execution_count": null,
"id": "f926ef9b",
"metadata": {
"vscode": {
"languageId": "r"
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},
"metadata": {},
"outputs": [],
"source": [
"! plink --bfile coatColor.binary --make-pheno coatColor.pheno \"yellow\" --assoc --reference-allele minor_alleles --allow-no-sex --adjust --dog --noweb --out coatColor"
Expand All @@ -380,11 +292,7 @@
"cell_type": "code",
"execution_count": null,
"id": "b94e1e2a",
"metadata": {
"vscode": {
"languageId": "r"
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"metadata": {},
"outputs": [],
"source": [
"%%bash\n",
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"cell_type": "code",
"execution_count": null,
"id": "60feed89",
"metadata": {
"gather": {
"logged": 1686582094642
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"vscode": {
"languageId": "r"
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},
"metadata": {},
"outputs": [],
"source": [
"#make a new library and install qqman their\n",
Expand All @@ -441,14 +342,7 @@
"cell_type": "code",
"execution_count": null,
"id": "a7e8cd2b",
"metadata": {
"gather": {
"logged": 1686584355516
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"vscode": {
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"metadata": {},
"outputs": [],
"source": [
"#make sure you are still CD in GWAS, when you change kernel it may reset to home\n",
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"cell_type": "code",
"execution_count": null,
"id": "7946a3a7",
"metadata": {
"gather": {
"logged": 1686584356532
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"metadata": {},
"outputs": [],
"source": [
"require(qqman, lib = Sys.getenv(\"R_LIBS_USER\"))"
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"cell_type": "code",
"execution_count": null,
"id": "0d28ef2c",
"metadata": {
"gather": {
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"metadata": {},
"outputs": [],
"source": [
"data=read.table(\"coatColor.assoc\", header=TRUE)"
Expand All @@ -493,14 +373,7 @@
"cell_type": "code",
"execution_count": null,
"id": "8e5207be",
"metadata": {
"gather": {
"logged": 1686584368241
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"vscode": {
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"metadata": {},
"outputs": [],
"source": [
"data=data[!is.na(data$P),]"
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"cell_type": "code",
"execution_count": null,
"id": "6330b1e0",
"metadata": {
"gather": {
"logged": 1686584371278
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"metadata": {},
"outputs": [],
"source": [
"manhattan(data, p = \"P\", col = c(\"blue4\", \"orange3\"),\n",
Expand Down Expand Up @@ -561,32 +427,7 @@
"source": []
}
],
"metadata": {
"kernel_info": {
"name": "ir"
},
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
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"name": "R",
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"version": "4.3.2"
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"nteract": {
"version": "[email protected]"
}
},
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"nbformat": 4,
"nbformat_minor": 5
}
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