dsQTL

The dsQTL package is based on data released in conjunction with Degner et al. (2012), DNase I sensitivity QTLs are a major determinant of human expression variation.

This package provides access to data from a very high-resolution assay of chromatin accessibility. The data available here are the result of scoring a 100bp tiling of the human genome for DnaseI hypersensitivity, and retaining the top 5 percent of tiles, ranked by sensitivity. We use a RangedSummarizedExperiment to represent the information on tile location; note that there are 1.46 million tiles scored in this excerpt, so the object takes a fair amount of time to load on a MacBook Air.

> data(DHStop5_hg19)
> DHStop5_hg19
class: RangedSummarizedExperiment 
dim: 1465442 70 
metadata(2): MIAME annotation
assays(1): scores
rownames(1465442): dhs_chr1_10402 dhs_chr1_10502 ... dhs_chr22_51228236 
  dhs_chr22_51234736
rowData names(0):
colnames(70): NA18486 NA18498 ... NA19239 NA19257
colData names(9): naid one ... male isFounder

Provenance information is provided in the vignette, and includes:

The dsQTL package data structures DSQ_2 and 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.

The vignette also describes how SNP data from 1000 genomes VCF can be used to test for genetic associations with DnaseI hypersensitivity.