makePSN_RangeSets: Create patient similarity interaction networks based on range...
In BaderLab/netDx: Network-based patient classifier

Description Usage Arguments Details Value Examples

Create patient similarity interaction networks based on range sets

makePSN_RangeSets(
  gr,
  rangeSet,
  netDir = tempdir(),
  simMetric = "coincide",
  quorum = 2L,
  verbose = TRUE,
  numCores = 1L
)

`gr`	(GRanges) patient ranges. Metadata should contain: ID: (char) unique patient ID LOCUS_NAME: (comma-separated char) named ranges overlapped
`rangeSet`	(list) list of GRanges, one entry per range set. Key is the name of the range set, and value is a GRanges object with corresponding ranges
`netDir`	(char) path to directory where networks should be written
`simMetric`	(char) Similarity metric. Currently only 'coincide' is supported; two patients share an edge if they overlap elements in the the same gene set. E.g. Two patients with CNVs that overlap different genes of the same pathway would be related, but patients overlapping genes that don't share a pathway (or, more accurately, a named-set grouping) would not be related. The edge weight is therefore binary.
`quorum`	(integer) minimum number of patients in a network for the network to be constructed
`verbose`	(logical) print detailed messages
`numCores`	(integer) num cores for parallel processing

Creates patient similarity networks when data consist of genomic events associated with patients. Examples include CNV or indel data for patients. To generate networks from full matrices such gene expression data, use makePSN_NamedMatrix instead. Genomic ranges corresponding to events in patients (gr) should be named. One network is created per named range set (rangeSet). Each set reflects a group of related loci ; for example, genomic ranges associated with genes in the same cellular pathway. Currently, the only similarity measure supported is binary; two patients are related in a network N if they both overlap elements of set N.

Vector of network filenames

data(pathway_GR,cnv_GR)
### # example commented out to avoid build errors because of parallel
### # execution. Uncomment to run.
### netList <- makePSN_RangeSets(cnv_GR,pathway_GR,'.')