Table 1.
An example of the features available in PLATO and other common genomics software
| PLATO | PLINK4 | GCTA59 | R/bioconductora | |
|---|---|---|---|---|
| Association analysis | ||||
| Genome-wide association study | X | X | X | GenABEL60 |
| Environment-wide association study | X | PheWAS61 | ||
| Phenome-wide association study | X | PheWAS | ||
| Differential CNV burden analysis | X | R | ||
| Differential gene expression | X | ArrayTools62 | ||
| Gene set enrichment analysis | GSEA63 | |||
| Gene×gene interaction | X | X | SNPassoc64 | |
| Gene×environment interaction | X | X | X | CGEN65 |
| Differential rare variation analysis | X | R, podkat66 | ||
| Types of statistical tests | ||||
| Logistic Regression | X | X | R | |
| Linear Regression | X | X | R | |
| Firth Regression | X | GWASTools67 | ||
| Likelihood ratio test | X | X | R | |
| Auto-detect regression type | X | GenABEL | ||
| Mixed linear model association | X | GENESIS68 | ||
| Family-based association | X | gap69 | ||
| Estimation of variance explained | X | R | ||
| Polygenic modeling | gap | |||
| Meta-analysis | X | gap | ||
| Genetic encodings supported | ||||
| Additive encoding | X | X | X | GenABEL |
| Dominant encoding | X | X | GenABEL | |
| Recessive encoding | X | X | GenABEL | |
| Codominant encoding | X | X | SNPassoc | |
| Overdominant encoding | SNPassoc | |||
| Multiple test correction | ||||
| Bonferroni | X | X | R | |
| FDR | X | X | R | |
| Permutation | X | X | SNPassoc | |
| QC filtering | ||||
| Marker call rate | X | X | SNPRelate57 | |
| Sample call rate | X | X | SNPRelate | |
| MAF | X | X | X | SNPRelate |
| LD Pruning | X | X | SNPRelate | |
| IBD | X | X | SNPRelate | |
| PCA | X | X | SNPRelate | |
aBioconductor is a repository in R that includes many packages. While there may be other packages that perform the same or similar test, we have selected one for illustrative purposes