storeToStats {gQTLstats} | R Documentation |
extract a vector from store results as ff (out of memory reference); support statistical reductions
storeToQuantiles(store, field, probs=c(seq(0,.999,.001), 1-(c(1e-4,1e-5,1e-6,1e-7))), ids = NULL, ..., checkField = FALSE, filter=force) storeToHist(store, getter = function(x) as.numeric(S4Vectors::as.matrix(mcols(x)[, grep("permScore", names(mcols(x)))])), breaks, ids = NULL, filter = force) storeToFDR(store, xprobs = c(seq(0, 0.999, 0.001), 1 - (c(1e-04, 1e-05, 1e-06, 1e-07))), xfield = "chisq", getter = function(x) as.numeric(S4Vectors::as.matrix(mcols(x)[, grep("permScore", names(mcols(x)))])), filter = force, .id4coln=1, ids=NULL)
store |
instance of |
field |
character tag, length one, must be name of a numeric field in the result set (typically something like 'chisq' in the GRanges generated by cisAssoc) |
xfield |
as |
ids |
job ids to be used; if NULL, process all jobs |
breaks |
boundaries of histogram bins |
... |
supplied to makeRegistry for a temporary registry: typically will be a vector of package names if additional packages are needed to process results |
checkField |
if TRUE steps will be taken to verify that the tag to which 'field' evaluates is present in result in the first job |
probs |
numeric vector of probabilities with values in [0,1].
See |
xprobs |
percentiles of the empirical distribution of the association statistic at which FDR estimates are recorded. |
getter |
function of a single argument that extracts a numeric vector of association scores obtained under permutation |
x |
instance of FDRsupp |
filter |
function accepting and returning GRanges instance, executed when cisAssoc result is loaded to modify that result, defaults to no-op |
.id4coln |
job id to be used for initial probe to determine names of fields in mcols of all jobs |
uses current BatchJobs configuration to parallelize extraction; reduceResults could be used for a sequential solution
storeToQuantiles and storeToHist return objects analogous to those returned by stats::quantile and graphics::hist.
However, it should be noted that storeToQuantiles will use
the quantile.ff
of ffbase. For
vectors of modest length, this can disagree with results of
base::quantile by a few percent.
storeToFDR and storeToFDRByProbe return an instance of FDRsupp class
uses ffbase:::c.ff explicitly to concatenate outputs; there is no guarantee of order among elements
## Not run: stopifnot(require(geuvStore2)) require(BatchJobs) require(gQTLBase) store = makeGeuvStore2() library(doParallel) if (.Platform$OS.type == "windows") { registerDoSEQ() } else registerDoParallel(cores=max(c(detectCores()-1,1))) smchisq = storeToFf( store, "chisq", ids=store@validJobs[1:3]) smchisq if (.Platform$OS.type != "windows") { # avoid timeout qs = storeToQuantiles( store, "chisq", ids = store@validJobs[1:5], probs=seq(.1,.9,.1) ) qs hh = storeToHist( store, ids = store@validJobs[1:5], breaks= c(0,qs,1e9) ) hh$counts fd = storeToFDR( store, xprobs=c(seq(.05,.95,.05),.99,.999) ) tail(getTab(fd),4) sss = storeToFDRByProbe( store , xprobs=c(seq(.05,.95,.05),.99) ) tail(getTab(sss),4) } ## End(Not run)