qqStore: create a binned QQplot for a sharded store

In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies

Description

create a binned QQplot for a sharded store with association and permutation statistics

Usage

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", ...)

Arguments

st	instance of ciseStore-class
ids	optional job id vector; if NULL, all jobs used
.probs	vector of probabilities for use with quantile evaluation, as provided in ffbase, using storeToQuantiles
xlim.in	xlim setting for QQplot
lowfac	we use a log-log plot, and the first quantile (as prescribed in .probs) is often close to zero; we reassign it to lowfac*(second quantile)
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

Value

invisibly returns list with elements qx, qy, counts, fracs

Examples

## Not run: 
library(geuvStore2)
library(gQTLBase)
gs = makeGeuvStore2()
qqStore(gs) #, ids=partialIds()[1:20])

## End(Not run)

gQTLstats documentation built on Nov. 8, 2020, 7:53 p.m.