Instances from this class can be input to the transScores
function to control a trans-eQTL search.
Objects from the Class
Instances from this class can be input to the transScores
function to control a trans-eQTL search.
Objects can be created by calls of the form new("TransConfig").
Slots
snpchr:
Object of class "character"
identifies the name of the chromosome harboring
SNP that will all be used (subject
to filtering by smFilter function) in transcriptome-wide searches
for associated transcripts
gbufsize:
Object of class "integer",
scores for the top gbufsize genes are retained as the search proceeds
batchsize:
Object of class "integer"
used in processing ff-based archives for association scores
smpack:
Object of class "character",
tells the name of the installed package used for retrieval
of expression-genotype data using getSS
rhs:
Object of class "formula", formula
used in snp.rhs.tests; typically not used.
If plug-in FDR is desired,
adjustments should be executed in a regressOut call .
folderStem:
Object of class "character",
name of a folder where interim results are sequestered.
radius:
Object of class "integer",
defines region around SNP within which genes are considered 'cis' so
tests are not conducted.
shortfac:
Object of class "integer" see
documentation for CisConfig-class
chrnames:
Object of class "character" see
documentation for CisConfig-class
smchrpref:
Object of class "character" see
documentation for CisConfig-class
gchrpref:
Object of class "character" see
documentation for CisConfig-class
schrpref:
Object of class "character" see
documentation for CisConfig-class
geneApply:
Object of class "function" see
documentation for CisConfig-class
geneannopk:
Object of class "character" see
documentation for CisConfig-class
snpannopk:
Object of class "character" see
documentation for CisConfig-class
smFilter:
Object of class "function" see
documentation for CisConfig-class
exFilter:
Object of class "function" see
documentation for CisConfig-class
keepMapCache:
Object of class "logical" see
documentation for CisConfig-class
SSgen:
Object of class "function" see
documentation for CisConfig-class
excludeRadius:
Object of class "integerOrNULL" see
documentation for CisConfig-class
estimates:
Object of class "logical" see
documentation for CisConfig-class
Extends
Class "CisConfig", directly.
Methods
batchsize
signature(x = "TransConfig"): ...
batchsize<-
signature(object = "TransConfig", value = "integer"): ...
gbufsize
signature(x = "TransConfig"): ...
gbufsize<-
signature(object = "TransConfig", value = "integer"): ...
show
signature(object = "TransConfig"): ...
snpchr
signature(x = "TransConfig"): ...
snpchr<-
signature(object = "TransConfig", value = "character"): ...
Examples
showClass("TransConfig")
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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/TransConfig-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: TransConfig-class
> ### Title: Class '"TransConfig"'
> ### Aliases: TransConfig-class batchsize,TransConfig-method
> ### batchsize<-,TransConfig,integer-method gbufsize,TransConfig-method
> ### gbufsize<-,TransConfig,integer-method snpchr,TransConfig-method
> ### snpchr<-,TransConfig,character-method batchsize batchsize<- gbufsize
> ### gbufsize<- snpchr snpchr<- show,TransConfig-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("TransConfig")
Class "TransConfig" [package "GGtools"]
Slots:
Name: snpchr gbufsize batchsize smpack rhs
Class: character integer integer character formula
Name: nperm folderStem radius shortfac chrnames
Class: integer character integer integer character
Name: smchrpref gchrpref schrpref geneApply geneannopk
Class: character character character function character
Name: snpannopk smFilter exFilter keepMapCache SSgen
Class: character function function logical function
Name: genome excludeRadius estimates extraProps useME
Class: character integerOrNULL logical function logical
Name: MEpvot
Class: numeric
Extends: "CisConfig"
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.