qqStore {gQTLstats} | R Documentation

## create a binned QQplot for a sharded store

### 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)

[Package gQTLstats version 1.12.0 Index]