ciseqByCluster {GGtools} | R Documentation

## end-to-end cluster-based cis-eQTL search, and allied utilities

### Description

end-to-end cluster-based cis-eQTL search, and allied utilities

### Usage

    ciseqByCluster(cl, pack = "yri1kgv", outprefix = "yrirun",
      finaltag = "partyri100k", chromsToRun = 1:22,
      targetfolder = "/freshdata/YRI_3", radius = 100000L, nperm = 3L, ncoresPerNode = 8,
      numPCtoFilter = 10, lowerMAF = 0.02, geneannopk = "lumiHumanAll.db",
      snpannopk = "SNPlocs.Hsapiens.dbSNP144.GRCh37", smchrpref = "chr",
      tmpForSort = "/tmp", numtiles = 200,
      postProcCores = 12, reqlist = NULL)

### Arguments

`cl` | instance of S3 cluster class from parallel package
`pack` | character string naming package to which `getSS` can be applied to generate `smlSet-class` instances
`outprefix` | character string used to prefix names of output GFF3 files
`finaltag` | character string used to prefix names of final amalgamated GFF3 and data.table instances
`chromsToRun` | numeric tags of chromosomes to be analyzed
`targetfolder` | character string naming folder where GFF3 will be deposited
`radius` | extent of search around gene model in bp
`nperm` | number of permutations for plug-in FDR computation (usually a small integer)
`ncoresPerNode` | number of cores for multicore testing: chromosomes map to nodes, genes map to cores
`numPCtoFilter` | number of PCs to be removed through `clipPCs`
`lowerMAF` | lower bound on MAF of SNP to be included for testing
`geneannopk` | character string naming Bioconductor package with annotation for expression probe identifiers
`snpannopk` | character string naming Bioconductor package with annotation for SNP locations
`smchrpref` | character prefix converting chromsToRun elements to basenames of rda files harboring SnpMatrix instances
`tmpForSort` | the assembly of final resources employs unix sort, and substantial temporary space can be required; this parameter tells where the temp files will reside
`numtiles` | number of tiles into which the genome in use will be sliced for parallel processing in final assembly
`postProcCores` | numeric establishing number of cores to use for final assembly of annotated output
`reqlist` | rescue request, see Details section

### Details

purpose is to maximize throughput of cis-eQTL testing in a two-level concurrent computing environment, where a cluster as defined in package parallel has nodes to which half-chromosomes will be dispatched; each node is assumed to be multicore and genes are mapped to cores during the iteration process.

the reqlist parameter consists of a list of elements (chromosome name, subchromosome token, and handler) to be used for completing a partial run

### Value

a set of GFF3 files encoding all cis associations with location and various metadata

### See Also

`gffprocess`, `cgff2dt`

### Examples

    #none yet

[Package GGtools version 5.22.0 Index]