MediaWiki API result
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{
"warnings": {
"query": {
"*": "Formatting of continuation data has changed. To receive raw query-continue data, use the 'rawcontinue' parameter. To silence this warning, pass an empty string for 'continue' in the initial query."
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"batchcomplete": "",
"continue": {
"gapcontinue": "SEQPower_Exercise",
"continue": "gapcontinue||"
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"43": {
"pageid": 43,
"ns": 0,
"title": "Regression Exercise",
"revisions": [
{
"contentformat": "text/x-wiki",
"contentmodel": "wikitext",
"*": "__NOTITLE__\n==Regression exercise==\nIn R:\n\n load(\"dbp.R\")\n ls()\n dbp[1:5,]\n #\n result.snp12 = glm (affection ~ rs1112, family=binomial(\"logit\"), data=dbp)\n print (result.snp12)\n print ( class (result.snp12) )\n print ( summary(result.snp12) )\n #\n dev.geno = anova (result.snp12, test=\"Chi\")\n lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],\"Deviance\"], df=2, ncp=0, FALSE)\n print ( lrt.pvalue )\n #\n print ( summary(result.snp12)$coefficients )\n snp.beta = summary(result.snp12)$coefficients[2:3,1]\n print ( snp.beta )\n print ( exp(snp.beta) )\n ci = confint (result.snp12)\n print (ci)\n print ( exp(ci) )\n #\n snp.data = dbp[,c(\"affection\", \"rs1112\")]\n summary(snp.data)\n snp.data[,\"rs1112\"] <- as.numeric(snp.data[,\"rs1112\"]) - 1<br />summary(snp.data)\n #\n result.all = glm (affection ~ rs1112, family=binomial(\"logit\"), data=snp.data)\n dev.all = anova (result.all, test=\"Chi\")\n summary(result.all)\n print(dev.all)\n #\n snp.data = dbp[,c(\"affection\", \"trait\",\"sex\", \"age\", \"rs1112\", \"rs1117\")]\n summary(snp.data)\n snp.data[,\"rs1112\"] <- as.numeric(snp.data[,\"rs1112\"]) - 1<br />snp.data[,\"rs1117\"] <- as.numeric(snp.data[,\"rs1117\"]) - 1\n #\n result.adj = glm (affection ~ sex + rs1112 , family=binomial(\"logit\"), data=snp.data)\n summary(result.adj)\n #\n result.adj = glm (affection ~ age + rs1112 , family=binomial(\"logit\"), data=snp.data)\n summary(result.adj)\n #\n result.adj = glm (affection ~ sex + age + rs1112, family=binomial(\"logit\"), data=snp.data)\n summary(result.adj)\n #\n result.adj = glm (affection ~ rs1117 + rs1112, family=binomial(\"logit\"), data=snp.data)\n summary(result.adj)\n anova (result.adj, test=\"Chi\")\n result.adj = glm (affection ~ rs1112 + rs1117, family=binomial(\"logit\"), data=snp.data)\n summary(result.adj)\n anova (result.adj, test=\"Chi\")\n #\n result.adj = lm (trait ~ rs1112, data=snp.data)\n summary(result.adj)\n result.adj = lm (trait ~ sex + rs1112, data=snp.data)\n summary(result.adj)\n #\n result.inter = glm (affection ~ sex * rs1112, family=binomial(\"logit\"), data=snp.data)\n summary(result.inter)\n result.inter = glm (affection ~ age * rs1112, family=binomial(\"logit\"), data=snp.data)\n summary(result.inter)\n #\n result.inter = glm (affection ~ rs1112 * rs1117, family=binomial(\"logit\"), data=snp.data)\n summary(result.inter)\n #\n q()"
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},
"71": {
"pageid": 71,
"ns": 0,
"title": "SEQLinkage Commands in Exercise",
"revisions": [
{
"contentformat": "text/x-wiki",
"contentmodel": "wikitext",
"*": "__NOTITLE__\n\n==SEQLinkage Commands in Exercise==\n<pre>seqlink -h\nawk '{if ($0~/^#/) {print} else {{maf=substr($8,12)}; if (maf<=0.01) {print}}}' hearing_with_high_freq.vcf >hearing.vcf\nbgzip -c hearing.vcf >hearing.vcf.gz \ntabix -p vcf hearing.vcf.gz\nseqlink --fam hearing.fam --vcf hearing.vcf.gz --format MERLIN\nseqlink --fam hearing.fam --vcf hearing.vcf.gz --format MERLIN --output nocollapsing --bin 1\nseqlink --fam hearing.fam --vcf hearing.vcf.gz --format MERLIN --output completecollapsing --bin 0\nseqlink --fam hearing.fam --vcf hearing.vcf.gz --freq EXACSASMAF -o linkageanalysis -K 0.002 --moi AR -W 0 -M 1 --run-linkage\n</pre>"
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}
}
}