Object specifying configuration of cis-eQTL search, to be used
with All.cis
Objects from the Class
Objects can be created by calls of the form new("CisConfig").
Use replacement methods to update the fields.
Slots
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.
Methods
chrnames
signature(x = "CisConfig"): ...
chrnames<-
signature(object = "CisConfig", value = "character"): ...
estimates
signature(x = "CisConfig"): ...
estimates<-
signature(object = "CisConfig", value = "logical"): ...
excludeRadius
signature(x = "CisConfig"): ...
excludeRadius<-
signature(object = "CisConfig", value = "integer"): ...
exFilter
signature(x = "CisConfig"): ...
exFilter<-
signature(object = "CisConfig", value = "function"): ...
gchrpref
signature(x = "CisConfig"): ...
gchrpref<-
signature(object = "CisConfig", value = "character"): ...
geneannopk
signature(x = "CisConfig"): ...
geneannopk<-
signature(object = "CisConfig", value = "character"): ...
geneApply
signature(x = "CisConfig"): ...
geneApply<-
signature(object = "CisConfig", value = "function"): ...
initialize
signature(.Object = "CisConfig"): ...
keepMapCache
signature(x = "CisConfig"): ...
keepMapCache<-
signature(object = "CisConfig", value = "logical"): ...
radius
signature(x = "CisConfig"): ...
radius<-
signature(object = "CisConfig", value = "integer"): ...
rhs
signature(x = "CisConfig"): ...
rhs<-
signature(object = "CisConfig", value = "function"): ...
schrpref
signature(x = "CisConfig"): ...
schrpref<-
signature(object = "CisConfig", value = "character"): ...
shortfac
signature(x = "CisConfig"): ...
shortfac<-
signature(object = "CisConfig", value = "integer"): ...
show
signature(object = "CisConfig"): ...
smchrpref
signature(x = "CisConfig"): ...
smchrpref<-
signature(object = "CisConfig", value = "character"): ...
smFilter
signature(x = "CisConfig"): ...
smFilter<-
signature(object = "CisConfig", value = "function"): ...
snpannopk
signature(x = "CisConfig"): ...
snpannopk<-
signature(object = "CisConfig", value = "character"): ...
SSgen
signature(x = "CisConfig"): ...
SSgen<-
signature(object = "CisConfig", value = "function"): ...
Examples
showClass("CisConfig")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(GGtools)
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: parallel
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following objects are masked from 'package:Matrix':
colMeans, colSums, expand, rowMeans, rowSums
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Attaching package: 'IRanges'
The following object is masked from 'package:data.table':
shift
Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db
Loading required package: org.Hs.eg.db
Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene
Attaching package: 'GGtools'
The following object is masked from 'package:stats':
getCall
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GGtools/CisConfig-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: CisConfig-class
> ### Title: Class '"CisConfig"'
> ### Aliases: buildConfList CisConfig-class genome,CisConfig-method
> ### genome<-,CisConfig,character-method chrnames,CisConfig-method
> ### chrnames<-,CisConfig,character-method estimates,CisConfig-method
> ### estimates<-,CisConfig,logical-method excludeRadius,CisConfig-method
> ### excludeRadius<-,CisConfig,integer-method exFilter,CisConfig-method
> ### exFilter<-,CisConfig,function-method gchrpref,CisConfig-method
> ### gchrpref<-,CisConfig,character-method geneannopk,CisConfig-method
> ### geneannopk<-,CisConfig,character-method geneApply,CisConfig-method
> ### geneApply<-,CisConfig,function-method initialize,CisConfig-method
> ### keepMapCache,CisConfig-method keepMapCache<-,CisConfig,logical-method
> ### radius,CisConfig-method radius<-,CisConfig,integer-method
> ### rhs,CisConfig-method rhs<-,CisConfig,function-method
> ### schrpref,CisConfig-method schrpref<-,CisConfig,character-method
> ### shortfac,CisConfig-method shortfac<-,CisConfig,integer-method
> ### show,CisConfig-method smchrpref,CisConfig-method
> ### smchrpref<-,CisConfig,character-method smFilter,CisConfig-method
> ### smFilter<-,CisConfig,function-method snpannopk,CisConfig-method
> ### snpannopk<-,CisConfig,character-method SSgen,CisConfig-method
> ### SSgen<-,CisConfig,function-method chrnames chrnames<- estimates
> ### estimates<- excludeRadius excludeRadius<- exFilter exFilter<-
> ### gchrpref gchrpref<- geneannopk geneannopk<- geneApply geneApply<-
> ### initialize keepMapCache keepMapCache<- radius radius<- rhs rhs<-
> ### schrpref schrpref<- shortfac shortfac<- show smchrpref smchrpref<-
> ### smFilter smFilter<- snpannopk snpannopk<- SSgen SSgen<- genome
> ### genome<- genome<-,CisConfig-method extraProps extraProps<-
> ### extraProps,CisConfig-method extraProps<-,CisConfig,function-method
> ### excludeRadius<-,CisConfig,integerOrNULL-method
> ### folderStem,CisConfig-method folderStem<-,CisConfig,character-method
> ### nperm,CisConfig-method nperm<-,CisConfig,integer-method
> ### rhs<-,CisConfig,formula-method smpack,CisConfig-method
> ### smpack<-,CisConfig,character-method excludeRadius<- folderStem
> ### folderStem<- nperm nperm<- rhs<- smpack smpack<-
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("CisConfig")
Class "CisConfig" [package "GGtools"]
Slots:
Name: smpack rhs nperm folderStem radius
Class: character formula integer character integer
Name: shortfac chrnames smchrpref gchrpref schrpref
Class: integer character character character character
Name: geneApply geneannopk snpannopk smFilter exFilter
Class: function character character function function
Name: keepMapCache SSgen genome excludeRadius estimates
Class: logical function character integerOrNULL logical
Name: extraProps useME MEpvot
Class: function logical numeric
Known Subclasses: "TransConfig"
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.