descriptive plot of expression against genotype for cisAssoc results

Description

descriptive plot of expression against genotype for cisAssoc results

Usage

eqBox(gene, snp, se, tf, radius=1e6, genome="hg19", ...)
eqDesc(gene, snp, se, tf, radius=1e6, genome="hg19", ...)

Arguments

Details

The chromosome names in the VCF and the seqlevelsStyle of the Summarized Experiment must match.

Value

eqBox produces a boxplot for all categories (including NA) of genotype. eqDesc tabulates the genotype calls in categories.

Examples

if (require(VariantAnnotation)) {
 data(lgeu)
 lgeue = lgeu[,which(lgeu$popcode=="CEU")]
 tf20 = TabixFile(system.file("vcf/c20exch.vcf.gz", package="GGtools"))
 eqBox( "ENSG00000126005.10", "rs2425038", lgeue, tf20 )
 }

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 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/eqBox.Rd_%03d_medium.png", width=480, height=480)
> ### Name: eqBox
> ### Title: descriptive plot of expression against genotype for cisAssoc
> ###   results
> ### Aliases: eqBox eqDesc
> ### Keywords: models
> 
> ### ** Examples
> 
> if (require(VariantAnnotation)) {
+  data(lgeu)
+  lgeue = lgeu[,which(lgeu$popcode=="CEU")]
+  tf20 = TabixFile(system.file("vcf/c20exch.vcf.gz", package="GGtools"))
+  eqBox( "ENSG00000126005.10", "rs2425038", lgeue, tf20 )
+  }
Loading required package: VariantAnnotation
Loading required package: SummarizedExperiment
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

Warning message:
In .local(x, ...) : non-diploid variants are set to NA
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>