Covariate-mediated adjustment of classification aids in the discrimination of background and enriched regions. (a) The local background (BG) estimate (red line) approximates a CNV detected by FAIRE-seq (black line) within a 2-Mbp region of chromosome 20 in MCF-7 cells. (b) Density plot of the window read counts for FAIRE-seq data in MCF-7 (chromosome 20) versus the posterior probability of a given window being classified as enriched, which included the local background estimate as a covariate in the ZINBA model formulation. The red box highlights a set of windows with high read counts (CNV background) being assigned a low posterior probability of being enriched. (c) The read overlap representation of MCF-7 FAIRE-seq data for all of chromosome 20 (top row) is displayed in the UCSC Genome Browser. The bottom panels zoom in on the black box outlining a CNV (same as panel (a)). Here a set of peak calls by F-Seq, MACS and ZINBA are shown as black boxes along with the FAIRE-seq data displayed using either an extended (top) or standard y-axis.
Rashid et al. Genome Biology 2011 12:R67 doi:10.1186/gb-2011-12-7-r67