R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 38 found.
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All.cis (Package: GGtools) :

function that computes score tests for all SNP cis to genes, with flexible filtering

● Data Source: BioConductor
● Keywords: models
● Alias: All.cis, add878, addgwhit, chrFilter, cisScores, inflammFilter, mcwAllCis-class, show,mcwAllCis-method
● 0 images

CisConfig-class (Package: GGtools) : Class code{"CisConfig"

Object specifying configuration of cis-eQTL search, to be used with All.cis

● Data Source: BioConductor
● Keywords: classes
● Alias: CisConfig-class, SSgen, SSgen,CisConfig-method, SSgen<-, SSgen<-,CisConfig,function-method, buildConfList, chrnames, chrnames,CisConfig-method, chrnames<-, chrnames<-,CisConfig,character-method, estimates, estimates,CisConfig-method, estimates<-, estimates<-,CisConfig,logical-method, exFilter, exFilter,CisConfig-method, exFilter<-, exFilter<-,CisConfig,function-method, excludeRadius, excludeRadius,CisConfig-method, excludeRadius<-, excludeRadius<-,CisConfig,integer-method, extraProps, extraProps,CisConfig-method, extraProps<-, extraProps<-,CisConfig,function-method, gchrpref, gchrpref,CisConfig-method, gchrpref<-, gchrpref<-,CisConfig,character-method, geneApply, geneApply,CisConfig-method, geneApply<-, geneApply<-,CisConfig,function-method, geneannopk, geneannopk,CisConfig-method, geneannopk<-, geneannopk<-,CisConfig,character-method, genome, genome,CisConfig-method, genome<-, genome<-,CisConfig,character-method, genome<-,CisConfig-method, initialize, initialize,CisConfig-method, keepMapCache, keepMapCache,CisConfig-method, keepMapCache<-, keepMapCache<-,CisConfig,logical-method, radius, radius,CisConfig-method, radius<-, radius<-,CisConfig,integer-method, rhs, rhs,CisConfig-method, rhs<-, rhs<-,CisConfig,function-method, schrpref, schrpref,CisConfig-method, schrpref<-, schrpref<-,CisConfig,character-method, shortfac, shortfac,CisConfig-method, shortfac<-, shortfac<-,CisConfig,integer-method, show, show,CisConfig-method, smFilter, smFilter,CisConfig-method, smFilter<-, smFilter<-,CisConfig,function-method, smchrpref, smchrpref,CisConfig-method, smchrpref<-, smchrpref<-,CisConfig,character-method, snpannopk, snpannopk,CisConfig-method, snpannopk<-, snpannopk<-,CisConfig,character-method
● 0 images

EqAppr-class (Package: GGtools) : Class code{"EqAppr"

Manage the appraisal of an eQTL search

● Data Source: BioConductor
● Keywords: classes
● Alias: EqAppr-class, calfig, calfig,EqAppr,character-method, getModnames,EqAppr-method, getPruned,EqAppr-method, getSens,EqAppr-method, getUnpruned,EqAppr-method, show,ApprRes-method, show,EqAppr-method
● 0 images

GGtools-package (Package: GGtools) :

software and data for analyses in genetics of gene expression

● Data Source: BioConductor
● Keywords: package
● Alias: GGtools, GGtools-package, hg19.si.df
● 0 images

TransConfig-class (Package: GGtools) : Class code{"TransConfig"

Instances from this class can be input to the transScores function to control a trans-eQTL search.

● Data Source: BioConductor
● Keywords: classes
● Alias: TransConfig-class, batchsize, batchsize,TransConfig-method, batchsize<-, batchsize<-,TransConfig,integer-method, gbufsize, gbufsize,TransConfig-method, gbufsize<-, gbufsize<-,TransConfig,integer-method, show,TransConfig-method, snpchr, snpchr,TransConfig-method, snpchr<-, snpchr<-,TransConfig,character-method
● 0 images

appraise (Package: GGtools) :

appraisal for eQTL prediction models

● Data Source: BioConductor
● Keywords: models
● Alias: appraise, bindgwava
● 0 images

best.cis.eQTLs (Package: GGtools) :

collect genewise best scoring eQTL

● Data Source: BioConductor
● Keywords: models
● Alias: All.cis.eQTLs, allSigCis-class, best.cis.eQTLs, chromsUsed, chromsUsed,mcwBestCis-method, fdr, fullreport, fullreport,mcwBestCis,character-method, fullreport,mcwBestCis,missing-method, getAll, getBest, getCall, mcwBestCis-class, meta.All.cis.eQTLs, meta.best.cis.eQTLs, show,allCigCis-method, show,allSigCis-method, show,cwBestCis-method, show,mcwBestCis-method
● 0 images

best.trans.eQTLs (Package: GGtools) :

collect strongest trans SNP-gene associations in a buffer of size K genes per SNP

● Data Source: BioConductor
● Keywords: models
● Alias: best.trans.eQTLs
● 0 images

bindmaf (Package: GGtools) :

bind testing metadata to a best.cis.eQTLs result

● Data Source: BioConductor
● Keywords: models
● Alias: meta.bindmaf
● 0 images

cgff2dt (Package: GGtools) :

translate the GFF3 from a ciseqByCluster/processgff output into a serialized data.table instance, compute genome-wide plug-in FDR, and update the GFF3 with this FDR

● Data Source: BioConductor
● Keywords: models
● Alias: cgff2dt
● 0 images