Table 1 Methods included in the package
From: ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
Method | Ref. | Type a | Hypothesis | A/I b | Primary Graph | Implementation | Input data c |
|---|---|---|---|---|---|---|---|
TopologyGSA | [14] | M | self-contained | No | DAG | adjusted | GEDM |
DEGraph | [16] | M | self-contained | Yes | DAG | adjusted | GEDM |
clipper | [15] | M | self-contained | No | DAG | adjusted | GEDM |
SPIA | [17], | U | competitive | Yes | directed | adjusted | DEG and their log fold-change |
| Â | [25] | Â | Â | Â | Â | Â | Â |
PRS | [26] | U | competitive | No | directed | de novo | DEG and their log-fold change |
PWEA | [27] | U | competitve | No | undirected | de novo | gene-level statistics |
TAPPA | [8] | U | self-contained | No | undirected | de novo | GEDM |