Skip to contents

Get Association P-values

Source: R/AllGenerics.R, R/AllClasses.R
pval.Rd

Extract the association p-value vector from a GwasSumStats or QtlSumStats entry, selected by its identity tuple. Part of the first-class summary-statistic column set alongside z / coef / se.

Usage

pval(x, ...)

# S4 method for class 'SumStatsBase'
pval(
  x,
  studyName = NULL,
  context = NULL,
  trait = NULL,
  annotateSignificance = NULL,
  ranges = NULL
)

Arguments

x

A GwasSumStats or QtlSumStats object.

...

Class-specific selection arguments.

studyName

Character (length 1) or NULL. Restrict the selection to this study; NULL matches all studies.

context

Character (length 1) or NULL. Restrict the selection to this context; NULL matches all contexts.

trait

Character (length 1) or NULL. Restrict the selection to this trait; NULL matches all traits.

annotateSignificance

Optional correction-method name passed through to sumStats (QTL only); NULL applies none.

ranges

A GRanges or NULL (default). Return only the variants overlapping these ranges; NULL returns everything.

Value

Numeric vector of p-values, or NULL if not available.

Examples

data(qtlSumStatsExample)
pval(qtlSumStatsExample)
#> NULL