ciseqByCluster: end-to-end cluster-based cis-eQTL search, and allied...
In GGtools: software and data for analyses in genetics of gene expression

Description Usage Arguments Details Value See Also Examples

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

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)

`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

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

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

gffprocess, cgff2dt