Man pages for isglobal-brge/SNPassoc
SNPs-Based Whole Genome Association Studies
| association | Association analysis between a single SNP and a given... |
| asthma | SNP data on asthma case-control study |
| BonferroniSig | Bonferroni correction of p values |
| GenomicControl | Population substructure |
| getGeneSymbol | Get gene symbol from a list of SNPs |
| getNiceTable | Get Latex output |
| getSignificantSNPs | Extract significant SNPs from an object of class... |
| haplointeraction | Haplotype interaction with a covariate |
| HapMap | SNPs from HapMap project |
| HapMap.SNPs.pos | SNPs from HapMap project |
| inheritance | Collapsing (or recoding) genotypes into different categories... |
| int | Identify interaction term |
| interactionPval | Two-dimensional SNP analysis for association studies |
| intervals | Print ORs and 95% confidence intervals for an object of class... |
| isMonomorphic | Check whether a SNP is Monomorphic |
| LD | max-statistic for a 2x3 table |
| makegeno | Create a group of locus objects from some SNPs, assign to... |
| maxstat | max-statistic for a 2x3 table |
| odds | Extract odds ratios, 95% CI and pvalues |
| permTest | Permutation test analysis |
| plotMissing | Plot of missing genotypes |
| plotWGassociation | Function to plot -log p values from an object of class... |
| qqpval | Functions for inspecting population substructure |
| related | Get related samples |
| resHapMap | SNPs from HapMap project |
| scanWGassociation | Whole genome association analysis |
| setupSNP | Convert columns in a dataframe to class 'snp' |
| snp | SNP object |
| SNPassoc-internal | Internal SNPstat functions |
| SNPs | SNPs in a case-control study |
| SNPs.info.pos | SNPs in a case-control study |
| sortSNPs | Sort a vector of SNPs by genomic position |
| tableHWE | Test for Hardy-Weinberg Equilibrium |
| Tablemeanse | Descriptive sample size, mean, and standard error |
| TableNPer | Descriptive sample size and percentage |
| WGassociation | Whole genome association analysis |
