%\VignetteIndexEntry{dsQTL, data excerpt from Degner et al. 2012 Nature letter} %\VignetteDepends{dsQTL, Biobase, SummarizedExperiment, GGBase, GGtools, rtracklayer} %\VignetteKeywords{genetics, Expression Analysis} %\VignettePackage{dsQTL} % % NOTE -- ONLY EDIT THE .Rnw FILE!!! The .tex file is % likely to be overwritten. % \documentclass[12pt]{article} \usepackage{amsmath,pstricks} \usepackage{auto-pst-pdf} \usepackage[authoryear,round]{natbib} \usepackage{hyperref} \textwidth=6.2in \textheight=8.5in %\parskip=.3cm \oddsidemargin=.1in \evensidemargin=.1in \headheight=-.3in \newcommand{\scscst}{\scriptscriptstyle} \newcommand{\scst}{\scriptstyle} \newcommand{\Rfunction}[1]{{\texttt{#1}}} \newcommand{\Robject}[1]{{\texttt{#1}}} \newcommand{\Rpackage}[1]{{\textit{#1}}} \newcommand{\Rmethod}[1]{{\texttt{#1}}} \newcommand{\Rfunarg}[1]{{\texttt{#1}}} \newcommand{\Rclass}[1]{{\textit{#1}}} \textwidth=6.2in \bibliographystyle{plainnat} \begin{document} %\setkeys{Gin}{width=0.55\textwidth} \title{dsQTL: exploring DNA-variants associated with DNaseI hypersensitivity} \author{VJ Carey} \maketitle \section{Introduction} Degner et al. (2012) publish information on associations between DNA variants (SNP, SNV, and indels) and DNaseI hypersensitivity measures acquired via DNase-Seq. This package includes information from the Chicago group on normalized DNase-seq data for chromosomes 2 and 17, and genotype data from chromosome 2 only. \section{The basic data structure} <>= library(dsQTL) data(DSQ_17) metadata(DSQ_17) metadata(DSQ_17)[[1]] @ We use summarized experiment structure for the assay data, but the imputed genotype data are kept separate, in the package, in the inst/parts folder. The data structure on chr2, which will be used to reproduce some findings, is more mature <>= data(DSQ_2) names(assays(DSQ_2)) assays(DSQ_2)[[1]][1:5,1:5] rowRanges(DSQ_2) @ To implement the GGBase protocol for on-the-fly generation of smlSet instances from getSS queries, we have an ExpressionSet instance with specific names. <>= data(eset, package="dsQTL") ex @ The genotype data supplied by Degner et al are imputed to 1000 genomes haplotypes, and are reals in [0,2]. For simplicity the current image of the data uses the rounding of the fractional genotypes x with round(x,0). The feature data refer to the retained 100bp segments that were summarized for DNaseI hypersensitivity and found to lie in the uppermost 5\% of the distribution. <>= library(Biobase) fData(ex)[1:5,,drop=FALSE] @ We can get the integrated container as <>= library(GGBase) ds2 = getSS("dsQTL", "roundGT_2") @ the name indicates that we simply rounded the imputed fractional genotypes to nearest integer. A very restricted search is: <>= # need to get rid of SNPlocs package getSNPlocs getSNPlocs = dsQTL::getSNPlocs # force library(GGtools) #library(parallel) #options(mc.cores=12) n1 = best.cis.eQTLs(smpack="dsQTL", radius=2000, geneannopk="dsQTL", snpannopk="dsQTL", chrnames="2", smchrpref="roundGT_", smFilter = function(x) GTFfilter(x, lower=0.05)[23810:23830,], # geneApply=mclapply) geneApply=lapply) <>= n1 @ <>= plot_EvG(probeId("dhs_2_45370802"), rsid("chr2.45370846"), getSS("dsQTL", "roundGT_2", wrapperEndo=function(x){annotation(x)="dsQTL"; x})) @ \section{Provenance} \subsection{Normed DNaseI hypersensitivity scores} The dsQTL package data structures \verb+DSQ_2+ and \verb+DSQ_17+ are generated from GEO GSE31388, from which a collection of 70 compressed BED format files were acquired Aug 9 2011. These are imported using the rtracklayer package to obtain location and score information for all the recorded DNaseI hypersensitivity assay results. For example, after import for NA19257, we have \begin{verbatim} Browse[1]> x [1] "NA19257" Browse[1]> tmp RangedData with 1465907 rows and 3 value columns across 22 spaces space ranges | name score strand | 1 chr1 [ 402, 501] | NOT -0.67088720 + 2 chr1 [ 502, 601] | NOT -1.69969288 + 3 chr1 [ 602, 701] | NOT 0.13520754 + ... ... ... ... ... ... ... 1465905 chr22 [49571602, 49571701] | NOT 0.62742318 + 1465906 chr22 [49575102, 49575201] | NOT -0.09417379 + 1465907 chr22 [49581602, 49581701] | NOT -0.29496269 + \end{verbatim} The scores for locations on chromosome 2 were collected using <>= proc1 = function(x) { library(rtracklayer) tmp = import(paste(x, ".qnorm.bed.gz", sep="")) stt = split(tmp, space(tmp)) obn = paste(x, "_dsq_chr2", sep="") assign(obn, stt[["chr2"]]) save(list=obn, file=paste(obn, ".rda", sep="")) NULL } @ The regions and scores reported are described in the GEO metadata as \begin{quotation} We also provide BED file format data for each individual for the top 5\% of the genome in terms of total sensitivity. This data was mapped to hg18 using a custom read-mapping algorithm which we describe in detail in the associated publication. Measures of DNase sensitivity were quantile normalized within each individual to a standard normal distribution. Each individual was corrected for GC bias and the top 4 principle (sic) components were removed from the data (See manuscript). \end{quotation} Score data were structured as a matrix with columns corresponding to Yoruba HapMap subject, and rows corresponding to reported hypersensitivity regions. The \texttt{RangedSummarizedExperiment} container is used to unite range and score data in the assays component, and allied metadata are available in metadata and colData components. \subsection{Genotype data} Textual representation of the allelic doses is provided at \url{http://eqtl.uchicago.edu/dsQTL_data/GENOTYPES/}. As of Oct 2012, these were rounded to allele counts to allow use of snpMatrix representation for chromosome 2 genotypes; propagation of dosage fractions will be undertaken in late 2012. \section{Session information} <>= sessionInfo() @ \end{document}