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
