Description Objects from the Class Slots Methods Examples
Object specifying configuration of cis-eQTL search, to be used with All.cis
Objects can be created by calls of the form new("CisConfig")
.
Use replacement methods to update the fields.
smpack
:character string identifying package
holding the expression and genotype data; see getSS
genome
:character string identifying genome build in use
rhs
:Object of class "formula"
right hand
side for calls to snp.rhs.tests
nperm
:Object of class "integer"
number of permutations for plug in FDR
folderStem
:Object of class "character"
string used for scratch space folders, relative to current folder
radius
:Object of class "integer"
radius
of search
shortfac
:Object of class "integer"
scores are scaled up by this factor so that precision can
be retained in short integer representation
chrnames
:Object of class "character"
string identifying chromosome label used in gene annotation
retrieval – typically length 1
smchrpref
:Object of class "character"
prefix to be attached to chromosome label in chrnames
to pick out the element of smlSet-class
instance
used in testing
gchrpref
:Object of class "character"
prefix
on chrnames token to be used for gene location retrievals
schrpref
:Object of class "character"
prefix
on chrnames token to be used with SNPlocs package for
retrieval of SNP locations
geneApply
:Object of class "function"
iterator
over genes, could be lapply or mclapply
geneannopk
:Object of class "character"
Bioconductor
annotation package for gene locations, typically for expression array
snpannopk
:Object of class "character"
Bioconductor
dbSNP annotation package
smFilter
:Object of class "function"
function
to be applied to smlSet instance that yields an smlSet instance with
required contents; could apply MAF restriction for example by calling
MAFfilter
exFilter
:Object of class "function"
function
that is run right after smlSet is materialized, permitting replacement
or filtering of expression data, when, for example, the ExpressionSet
includes multiple tissue types
keepMapCache
:Object of class "logical"
for
enhancing processing of gene-SNP cis mapping with a global cache
SSgen
:Object of class "function"
function
that accepts name of an expression+SnpMatrix package (as generated
by externalize
), a chromosome tag (chrnames
prefixed by smchrpref
), and a function, and returns
an smlSet instance
excludeRadius
:Object of class "integerOrNULL"
which will determine what interval about the gene is excluded for
cis testing; 0 should exclude all within-gene SNP, but needs
testing
estimates
:Object of class "logical"
if TRUE,
estimates and standard errors (expanded and reduced in storage
as a short int, using shortfac
) are generated and retained
extraProps
:Object of class "function"
this function is applied to the cisScores output
before it is returned, to bind additional metadata
to the ranges if desired. Defaults to function(x)x.
useME
:Object of class "logical"
if TRUE,
use the statistics generated by Matrix_eQTL_engine
for
association testing.
MEpvot
:Object of class "numeric"
used
if useME
slot is set to TRUE: p-value output threshold
for retaining association test statistic generated by
Matrix_eQTL_engine
; defaults to 0.5. Higher values
lead to higher volumes and longer times to completion.
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "character")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "logical")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "integer")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "function")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "character")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "character")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "function")
: ...
signature(.Object = "CisConfig")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "logical")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "integer")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "function")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "character")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "integer")
: ...
signature(object = "CisConfig")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "character")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "function")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "character")
: ...
signature(x = "CisConfig")
: ...
signature(object = "CisConfig", value = "function")
: ...
1 | showClass("CisConfig")
|
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