eqtlTestsManager-class: Class '"eqtlTestsManager"'

In GGtools: software and data for analyses in genetics of gene expression

Description

manage out-of-memory elements of an eQTL search

Objects from the Class

Objects can be created by calls of the form new("eqtlTestsManager", ...).

Slots

fffile:

Object of class "ff_matrix" chisquared statistics stored as short ints in ff out of memory file

call:

Object of class "call" audit of creation call

sess:

Object of class "ANY" session info structure at time of creation

exdate:

Object of class "ANY" date at time of creation

shortfac:

Object of class "numeric" number by which chisq stats are multiplied to allow recovery of precision

geneanno:

Object of class "character" string naming annotation package relevant for probe identifier translation

df:

Object of class "numeric" degrees of freedom of chisq stats

summaryList:

Object of class "list" list of genotype statistical summaries

Methods

[

signature(x = "eqtlTestsManager", i = "ANY", j = "ANY", drop = "ANY"): extract chisq statistics properly rescaled from short int to double

show

signature(object = "eqtlTestsManager"): concise report

topFeats

signature(feat = "probeId", mgr = "eqtlTestsManager"): extract highest scores for SNP associated with given probeId

topFeats

signature(feat = "rsid", mgr = "eqtlTestsManager"): extract highest scores for probes associated with given SNP

Note

instances are created by eqtlTests

Author(s)

VJ Carey <[e-mail]>

Examples

showClass("eqtlTestsManager")

GGtools documentation built on Nov. 8, 2020, 6:32 p.m.