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February 2, 2019 03:51
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Go analysis in R
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "Loading required package: BiocGenerics\n", | |
| "Loading required package: parallel\n", | |
| "\n", | |
| "Attaching package: ‘BiocGenerics’\n", | |
| "\n", | |
| "The following objects are masked from ‘package:parallel’:\n", | |
| "\n", | |
| " clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,\n", | |
| " clusterExport, clusterMap, parApply, parCapply, parLapply,\n", | |
| " parLapplyLB, parRapply, parSapply, parSapplyLB\n", | |
| "\n", | |
| "The following objects are masked from ‘package:stats’:\n", | |
| "\n", | |
| " IQR, mad, sd, var, xtabs\n", | |
| "\n", | |
| "The following objects are masked from ‘package:base’:\n", | |
| "\n", | |
| " anyDuplicated, append, as.data.frame, basename, cbind, colMeans,\n", | |
| " colnames, colSums, dirname, do.call, duplicated, eval, evalq,\n", | |
| " Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,\n", | |
| " lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,\n", | |
| " pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,\n", | |
| " rowSums, sapply, setdiff, sort, table, tapply, union, unique,\n", | |
| " unsplit, which, which.max, which.min\n", | |
| "\n", | |
| "Loading required package: graph\n", | |
| "Loading required package: Biobase\n", | |
| "Welcome to Bioconductor\n", | |
| "\n", | |
| " Vignettes contain introductory material; view with\n", | |
| " 'browseVignettes()'. To cite Bioconductor, see\n", | |
| " 'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'.\n", | |
| "\n", | |
| "Loading required package: GO.db\n", | |
| "Loading required package: AnnotationDbi\n", | |
| "Loading required package: stats4\n", | |
| "Loading required package: IRanges\n", | |
| "Loading required package: S4Vectors\n", | |
| "\n", | |
| "Attaching package: ‘S4Vectors’\n", | |
| "\n", | |
| "The following object is masked from ‘package:base’:\n", | |
| "\n", | |
| " expand.grid\n", | |
| "\n", | |
| "\n", | |
| "Loading required package: SparseM\n", | |
| "\n", | |
| "Attaching package: ‘SparseM’\n", | |
| "\n", | |
| "The following object is masked from ‘package:base’:\n", | |
| "\n", | |
| " backsolve\n", | |
| "\n", | |
| "\n", | |
| "groupGOTerms: \tGOBPTerm, GOMFTerm, GOCCTerm environments built.\n", | |
| "\n", | |
| "Attaching package: ‘topGO’\n", | |
| "\n", | |
| "The following object is masked from ‘package:IRanges’:\n", | |
| "\n", | |
| " members\n", | |
| "\n", | |
| "\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "library(topGO)\n", | |
| "library(org.Hs.eg.db)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "\n", | |
| "Attaching package: ‘AnnotationHub’\n", | |
| "\n", | |
| "The following object is masked from ‘package:Biobase’:\n", | |
| "\n", | |
| " cache\n", | |
| "\n", | |
| "snapshotDate(): 2018-10-24\n", | |
| "downloading 0 resources\n", | |
| "loading from cache \n", | |
| " ‘/home/avi//.AnnotationHub/72902’\n", | |
| "\n", | |
| "Please see: help('select') for usage information\n" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "OrgDb object:\n", | |
| "| DBSCHEMAVERSION: 2.1\n", | |
| "| Db type: OrgDb\n", | |
| "| Supporting package: AnnotationDbi\n", | |
| "| DBSCHEMA: HUMAN_DB\n", | |
| "| ORGANISM: Homo sapiens\n", | |
| "| SPECIES: Human\n", | |
| "| EGSOURCEDATE: 2018-Oct11\n", | |
| "| EGSOURCENAME: Entrez Gene\n", | |
| "| EGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA\n", | |
| "| CENTRALID: EG\n", | |
| "| TAXID: 9606\n", | |
| "| GOSOURCENAME: Gene Ontology\n", | |
| "| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/\n", | |
| "| GOSOURCEDATE: 2018-Oct10\n", | |
| "| GOEGSOURCEDATE: 2018-Oct11\n", | |
| "| GOEGSOURCENAME: Entrez Gene\n", | |
| "| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA\n", | |
| "| KEGGSOURCENAME: KEGG GENOME\n", | |
| "| KEGGSOURCEURL: ftp://ftp.genome.jp/pub/kegg/genomes\n", | |
| "| KEGGSOURCEDATE: 2011-Mar15\n", | |
| "| GPSOURCENAME: UCSC Genome Bioinformatics (Homo sapiens)\n", | |
| "| GPSOURCEURL: \n", | |
| "| GPSOURCEDATE: 2018-Oct2\n", | |
| "| ENSOURCEDATE: 2018-Oct05\n", | |
| "| ENSOURCENAME: Ensembl\n", | |
| "| ENSOURCEURL: ftp://ftp.ensembl.org/pub/current_fasta\n", | |
| "| UPSOURCENAME: Uniprot\n", | |
| "| UPSOURCEURL: http://www.UniProt.org/\n", | |
| "| UPSOURCEDATE: Thu Oct 18 05:22:10 2018" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| }, | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "'select()' returned 1:1 mapping between keys and columns\n" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<thead><tr><th scope=col>SYMBOL</th><th scope=col>GENENAME</th></tr></thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><td>HLA-A </td><td>major histocompatibility complex, class I, A</td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "\\begin{tabular}{r|ll}\n", | |
| " SYMBOL & GENENAME\\\\\n", | |
| "\\hline\n", | |
| "\t HLA-A & major histocompatibility complex, class I, A\\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "SYMBOL | GENENAME | \n", | |
| "|---|\n", | |
| "| HLA-A | major histocompatibility complex, class I, A | \n", | |
| "\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " SYMBOL GENENAME \n", | |
| "1 HLA-A major histocompatibility complex, class I, A" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| }, | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "'select()' returned 1:many mapping between keys and columns\n" | |
| ] | |
| }, | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<thead><tr><th></th><th scope=col>SYMBOL</th><th scope=col>GO</th><th scope=col>EVIDENCE</th><th scope=col>ONTOLOGY</th></tr></thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><th scope=row>2</th><td>HLA-A </td><td>GO:0001916</td><td>IBA </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>3</th><td>HLA-A </td><td>GO:0002474</td><td>TAS </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>4</th><td>HLA-A </td><td>GO:0002476</td><td>IBA </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>5</th><td>HLA-A </td><td>GO:0002479</td><td>TAS </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>6</th><td>HLA-A </td><td>GO:0002480</td><td>TAS </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>14</th><td>HLA-A </td><td>GO:0006955</td><td>IBA </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>25</th><td>HLA-A </td><td>GO:0050776</td><td>TAS </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>27</th><td>HLA-A </td><td>GO:0060333</td><td>TAS </td><td>BP </td></tr>\n", | |
| "\t<tr><th scope=row>28</th><td>HLA-A </td><td>GO:0060337</td><td>TAS </td><td>BP </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "\\begin{tabular}{r|llll}\n", | |
| " & SYMBOL & GO & EVIDENCE & ONTOLOGY\\\\\n", | |
| "\\hline\n", | |
| "\t2 & HLA-A & GO:0001916 & IBA & BP \\\\\n", | |
| "\t3 & HLA-A & GO:0002474 & TAS & BP \\\\\n", | |
| "\t4 & HLA-A & GO:0002476 & IBA & BP \\\\\n", | |
| "\t5 & HLA-A & GO:0002479 & TAS & BP \\\\\n", | |
| "\t6 & HLA-A & GO:0002480 & TAS & BP \\\\\n", | |
| "\t14 & HLA-A & GO:0006955 & IBA & BP \\\\\n", | |
| "\t25 & HLA-A & GO:0050776 & TAS & BP \\\\\n", | |
| "\t27 & HLA-A & GO:0060333 & TAS & BP \\\\\n", | |
| "\t28 & HLA-A & GO:0060337 & TAS & BP \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "| <!--/--> | SYMBOL | GO | EVIDENCE | ONTOLOGY | \n", | |
| "|---|---|---|---|---|---|---|---|---|\n", | |
| "| 2 | HLA-A | GO:0001916 | IBA | BP | \n", | |
| "| 3 | HLA-A | GO:0002474 | TAS | BP | \n", | |
| "| 4 | HLA-A | GO:0002476 | IBA | BP | \n", | |
| "| 5 | HLA-A | GO:0002479 | TAS | BP | \n", | |
| "| 6 | HLA-A | GO:0002480 | TAS | BP | \n", | |
| "| 14 | HLA-A | GO:0006955 | IBA | BP | \n", | |
| "| 25 | HLA-A | GO:0050776 | TAS | BP | \n", | |
| "| 27 | HLA-A | GO:0060333 | TAS | BP | \n", | |
| "| 28 | HLA-A | GO:0060337 | TAS | BP | \n", | |
| "\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " SYMBOL GO EVIDENCE ONTOLOGY\n", | |
| "2 HLA-A GO:0001916 IBA BP \n", | |
| "3 HLA-A GO:0002474 TAS BP \n", | |
| "4 HLA-A GO:0002476 IBA BP \n", | |
| "5 HLA-A GO:0002479 TAS BP \n", | |
| "6 HLA-A GO:0002480 TAS BP \n", | |
| "14 HLA-A GO:0006955 IBA BP \n", | |
| "25 HLA-A GO:0050776 TAS BP \n", | |
| "27 HLA-A GO:0060333 TAS BP \n", | |
| "28 HLA-A GO:0060337 TAS BP " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "# Mike's titorial for getting annotations\n", | |
| "library(\"AnnotationHub\")\n", | |
| "ah <- AnnotationHub()\n", | |
| "\n", | |
| "orgs <- subset(ah, ah$rdataclass == \"OrgDb\")\n", | |
| "orgdb <- query(orgs, \"Homo sapiens\")[[1]]\n", | |
| "\n", | |
| "orgdb\n", | |
| "\n", | |
| "select(orgdb, keys=\"HLA-A\", columns=\"GENENAME\", keytype=\"SYMBOL\")\n", | |
| "go <- select(orgdb, \"HLA-A\", \"GO\", \"SYMBOL\")\n", | |
| "go[go$ONTOLOGY == \"BP\",]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<thead><tr><th scope=col>ensembl_gene_id</th><th scope=col>go_id</th></tr></thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><td>ENSG00000147403</td><td> </td></tr>\n", | |
| "\t<tr><td>ENSG00000147403</td><td>GO:0003723 </td></tr>\n", | |
| "\t<tr><td>ENSG00000147403</td><td>GO:0016020 </td></tr>\n", | |
| "\t<tr><td>ENSG00000147403</td><td>GO:0006412 </td></tr>\n", | |
| "\t<tr><td>ENSG00000147403</td><td>GO:0005783 </td></tr>\n", | |
| "\t<tr><td>ENSG00000147403</td><td>GO:0005829 </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "\\begin{tabular}{r|ll}\n", | |
| " ensembl\\_gene\\_id & go\\_id\\\\\n", | |
| "\\hline\n", | |
| "\t ENSG00000147403 & \\\\\n", | |
| "\t ENSG00000147403 & GO:0003723 \\\\\n", | |
| "\t ENSG00000147403 & GO:0016020 \\\\\n", | |
| "\t ENSG00000147403 & GO:0006412 \\\\\n", | |
| "\t ENSG00000147403 & GO:0005783 \\\\\n", | |
| "\t ENSG00000147403 & GO:0005829 \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "ensembl_gene_id | go_id | \n", | |
| "|---|---|---|---|---|---|\n", | |
| "| ENSG00000147403 | | \n", | |
| "| ENSG00000147403 | GO:0003723 | \n", | |
| "| ENSG00000147403 | GO:0016020 | \n", | |
| "| ENSG00000147403 | GO:0006412 | \n", | |
| "| ENSG00000147403 | GO:0005783 | \n", | |
| "| ENSG00000147403 | GO:0005829 | \n", | |
| "\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " ensembl_gene_id go_id \n", | |
| "1 ENSG00000147403 \n", | |
| "2 ENSG00000147403 GO:0003723\n", | |
| "3 ENSG00000147403 GO:0016020\n", | |
| "4 ENSG00000147403 GO:0006412\n", | |
| "5 ENSG00000147403 GO:0005783\n", | |
| "6 ENSG00000147403 GO:0005829" | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "library(biomaRt)\n", | |
| "All.genes.Ens <- c(\"ENSG00000147403\")\n", | |
| "ensembl61 <- useMart( \"ENSEMBL_MART_ENSEMBL\", \n", | |
| " dataset = \"hsapiens_gene_ensembl\", \n", | |
| " host = \"www.ensembl.org\" )\n", | |
| "\n", | |
| "# ensembl61@attributes$\n", | |
| "\n", | |
| "test.GO.BP <- getBM(attributes = c(\"ensembl_gene_id\", \n", | |
| " \"go_id\"), \n", | |
| " filters = \"ensembl_gene_id\", \n", | |
| " values = All.genes.Ens,\n", | |
| " mart = ensembl61)\n", | |
| "head(test.GO.BP)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "#GO analysis\n", | |
| "All.genes.Ens <- c(\"ENSG00000147403\",\"ENSG00000184009\",\"ENSG00000259380\",\"ENSG00000253729\",\"ENSG00000163386\",\"ENSG00000113658\",\"ENSG00000182149\",\"ENSG00000149547\",\"ENSG00000055163\",\"ENSG00000161960\",\"ENSG00000147403\",\"ENSG00000055163\",\"ENSG00000132475\",\"ENSG00000161960\",\"ENSG00000196531\",\"ENSG00000174749\",\"ENSG00000149547\",\"ENSG00000210140\",\"ENSG00000133138\",\"ENSG00000251562\",\"ENSG00000206503\",\"ENSG00000181458\",\"ENSG00000248360\",\"ENSG00000055163\",\"ENSG00000169499\",\"ENSG00000139644\",\"ENSG00000168918\",\"ENSG00000133131\",\"ENSG00000161016\",\"ENSG00000234745\",\"ENSG00000269821\",\"ENSG00000112096\",\"ENSG00000249348\",\"ENSG00000210135\",\"ENSG00000171109\",\"ENSG00000104164\",\"ENSG00000151338\",\"ENSG00000206503\",\"ENSG00000176619\")\n", | |
| "geneList <- unique(read.table(\"./txp2gene.tsv\")['V2'])[, \"V2\"]\n", | |
| "topGenes <- All.genes.Ens\n", | |
| "geneListF <- factor(as.integer(geneList %in% topGenes))\n", | |
| "names(geneListF) <- geneList" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "\n", | |
| "Building most specific GOs .....\n", | |
| "\t( 12016 GO terms found. )\n", | |
| "\n", | |
| "Build GO DAG topology ..........\n", | |
| "\t( 16050 GO terms and 38068 relations. )\n", | |
| "\n", | |
| "Annotating nodes ...............\n", | |
| "\t( 18682 genes annotated to the GO terms. )\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "dat <- new(\"topGOdata\", \n", | |
| " ontology=\"BP\", \n", | |
| " allGenes=geneListF, \n", | |
| " nodeSize=10,\n", | |
| " annot=annFUN.org, \n", | |
| " mapping=\"org.Hs.eg.db\", \n", | |
| " ID=\"ensembl\")\n" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stderr", | |
| "output_type": "stream", | |
| "text": [ | |
| "\n", | |
| "\t\t\t -- Classic Algorithm -- \n", | |
| "\n", | |
| "\t\t the algorithm is scoring 1165 nontrivial nodes\n", | |
| "\t\t parameters: \n", | |
| "\t\t\t test statistic: fisher\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "res <- runTest(dat, algorithm=\"classic\", statistic=\"fisher\")" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 48, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/html": [ | |
| "<table>\n", | |
| "<thead><tr><th scope=col>GO.ID</th><th scope=col>Term</th><th scope=col>Annotated</th><th scope=col>Significant</th><th scope=col>Expected</th><th scope=col>classicFisher</th></tr></thead>\n", | |
| "<tbody>\n", | |
| "\t<tr><td>GO:0002252 </td><td>immune effector process </td><td>1292 </td><td> 8 </td><td>1.52 </td><td>6.8e-05 </td></tr>\n", | |
| "\t<tr><td>GO:0002638 </td><td>negative regulation of immunoglobulin pr...</td><td> 11 </td><td> 2 </td><td>0.01 </td><td>7.2e-05 </td></tr>\n", | |
| "\t<tr><td>GO:0002682 </td><td>regulation of immune system process </td><td>1655 </td><td> 8 </td><td>1.95 </td><td>0.00038 </td></tr>\n", | |
| "\t<tr><td>GO:0050778 </td><td>positive regulation of immune response </td><td> 916 </td><td> 6 </td><td>1.08 </td><td>0.00052 </td></tr>\n", | |
| "\t<tr><td>GO:0002701 </td><td>negative regulation of production of mol...</td><td> 41 </td><td> 2 </td><td>0.05 </td><td>0.00106 </td></tr>\n", | |
| "\t<tr><td>GO:0050776 </td><td>regulation of immune response </td><td>1124 </td><td> 6 </td><td>1.32 </td><td>0.00152 </td></tr>\n", | |
| "\t<tr><td>GO:0002376 </td><td>immune system process </td><td>3149 </td><td>10 </td><td>3.71 </td><td>0.00165 </td></tr>\n", | |
| "\t<tr><td>GO:0002480 </td><td>antigen processing and presentation of e...</td><td> 52 </td><td> 2 </td><td>0.06 </td><td>0.00169 </td></tr>\n", | |
| "\t<tr><td>GO:0006413 </td><td>translational initiation </td><td> 207 </td><td> 3 </td><td>0.24 </td><td>0.00177 </td></tr>\n", | |
| "\t<tr><td>GO:0002476 </td><td>antigen processing and presentation of e...</td><td> 58 </td><td> 2 </td><td>0.07 </td><td>0.00210 </td></tr>\n", | |
| "</tbody>\n", | |
| "</table>\n" | |
| ], | |
| "text/latex": [ | |
| "\\begin{tabular}{r|llllll}\n", | |
| " GO.ID & Term & Annotated & Significant & Expected & classicFisher\\\\\n", | |
| "\\hline\n", | |
| "\t GO:0002252 & immune effector process & 1292 & 8 & 1.52 & 6.8e-05 \\\\\n", | |
| "\t GO:0002638 & negative regulation of immunoglobulin pr... & 11 & 2 & 0.01 & 7.2e-05 \\\\\n", | |
| "\t GO:0002682 & regulation of immune system process & 1655 & 8 & 1.95 & 0.00038 \\\\\n", | |
| "\t GO:0050778 & positive regulation of immune response & 916 & 6 & 1.08 & 0.00052 \\\\\n", | |
| "\t GO:0002701 & negative regulation of production of mol... & 41 & 2 & 0.05 & 0.00106 \\\\\n", | |
| "\t GO:0050776 & regulation of immune response & 1124 & 6 & 1.32 & 0.00152 \\\\\n", | |
| "\t GO:0002376 & immune system process & 3149 & 10 & 3.71 & 0.00165 \\\\\n", | |
| "\t GO:0002480 & antigen processing and presentation of e... & 52 & 2 & 0.06 & 0.00169 \\\\\n", | |
| "\t GO:0006413 & translational initiation & 207 & 3 & 0.24 & 0.00177 \\\\\n", | |
| "\t GO:0002476 & antigen processing and presentation of e... & 58 & 2 & 0.07 & 0.00210 \\\\\n", | |
| "\\end{tabular}\n" | |
| ], | |
| "text/markdown": [ | |
| "\n", | |
| "GO.ID | Term | Annotated | Significant | Expected | classicFisher | \n", | |
| "|---|---|---|---|---|---|---|---|---|---|\n", | |
| "| GO:0002252 | immune effector process | 1292 | 8 | 1.52 | 6.8e-05 | \n", | |
| "| GO:0002638 | negative regulation of immunoglobulin pr... | 11 | 2 | 0.01 | 7.2e-05 | \n", | |
| "| GO:0002682 | regulation of immune system process | 1655 | 8 | 1.95 | 0.00038 | \n", | |
| "| GO:0050778 | positive regulation of immune response | 916 | 6 | 1.08 | 0.00052 | \n", | |
| "| GO:0002701 | negative regulation of production of mol... | 41 | 2 | 0.05 | 0.00106 | \n", | |
| "| GO:0050776 | regulation of immune response | 1124 | 6 | 1.32 | 0.00152 | \n", | |
| "| GO:0002376 | immune system process | 3149 | 10 | 3.71 | 0.00165 | \n", | |
| "| GO:0002480 | antigen processing and presentation of e... | 52 | 2 | 0.06 | 0.00169 | \n", | |
| "| GO:0006413 | translational initiation | 207 | 3 | 0.24 | 0.00177 | \n", | |
| "| GO:0002476 | antigen processing and presentation of e... | 58 | 2 | 0.07 | 0.00210 | \n", | |
| "\n", | |
| "\n" | |
| ], | |
| "text/plain": [ | |
| " GO.ID Term Annotated Significant\n", | |
| "1 GO:0002252 immune effector process 1292 8 \n", | |
| "2 GO:0002638 negative regulation of immunoglobulin pr... 11 2 \n", | |
| "3 GO:0002682 regulation of immune system process 1655 8 \n", | |
| "4 GO:0050778 positive regulation of immune response 916 6 \n", | |
| "5 GO:0002701 negative regulation of production of mol... 41 2 \n", | |
| "6 GO:0050776 regulation of immune response 1124 6 \n", | |
| "7 GO:0002376 immune system process 3149 10 \n", | |
| "8 GO:0002480 antigen processing and presentation of e... 52 2 \n", | |
| "9 GO:0006413 translational initiation 207 3 \n", | |
| "10 GO:0002476 antigen processing and presentation of e... 58 2 \n", | |
| " Expected classicFisher\n", | |
| "1 1.52 6.8e-05 \n", | |
| "2 0.01 7.2e-05 \n", | |
| "3 1.95 0.00038 \n", | |
| "4 1.08 0.00052 \n", | |
| "5 0.05 0.00106 \n", | |
| "6 1.32 0.00152 \n", | |
| "7 3.71 0.00165 \n", | |
| "8 0.06 0.00169 \n", | |
| "9 0.24 0.00177 \n", | |
| "10 0.07 0.00210 " | |
| ] | |
| }, | |
| "metadata": {}, | |
| "output_type": "display_data" | |
| } | |
| ], | |
| "source": [ | |
| "df <- GenTable(dat, classicFisher=res, topNodes=10)\n", | |
| "df" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "R", | |
| "language": "R", | |
| "name": "ir" | |
| }, | |
| "language_info": { | |
| "codemirror_mode": "r", | |
| "file_extension": ".r", | |
| "mimetype": "text/x-r-source", | |
| "name": "R", | |
| "pygments_lexer": "r", | |
| "version": "3.5.1" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
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