qqStore {gQTLstats} | R Documentation |
create a binned QQplot for a sharded store with association and permutation statistics
qqStore(st, ids = NULL, .probs = c(0, seq(0.6, 0.8, 0.2), 0.9, 0.95, 0.99, 0.999, 0.9999, 1), xlim.in = c(0.2, 75), lowfac = 0.5, xlab = "Permutation distribution", ylab = "Distribution of score statistic", countpos = 50, plot.it = TRUE, doab = TRUE, scoreField = "chisq", permField = "permScore_1", ...)
st |
instance of |
ids |
optional job id vector; if NULL, all jobs used |
.probs |
vector of probabilities for use with quantile evaluation,
as provided in ffbase, using |
xlim.in |
xlim setting for QQplot |
lowfac |
we use a log-log plot, and the first quantile (as prescribed
in |
xlab |
label |
ylab |
label |
countpos |
where on the x axis will we stack the information on bin counts |
plot.it |
logical, if FALSE, a list is returned with elements on quantile values and bin counts |
doab |
logical prescribing drawing of line of identity |
scoreField |
tag in store naming the statistic, typically 'chisq', can also be 'tstat' for GTEx |
permField |
tag in store naming the field holding statistics on realizations from permutation distribution |
... |
passed to storeToQuantiles |
invisibly returns list with elements qx, qy, counts, fracs
## Not run: library(geuvStore2) library(gQTLBase) gs = makeGeuvStore2() qqStore(gs) #, ids=partialIds()[1:20]) ## End(Not run)