Illustration of overlap (top) and adjacency (bottom) relationships.

<p>The <i>any</i> mode detects hits with partial or complete overlap, while <i>within</i> requires that the query range represents a subregion of the subject range.</p

Summary of the Ranges API.

<p>Categorized listing and description of the API for range-based objects, such as <i>IRanges</i>, <i>RangesList</i>, <i>GRanges</i> and <i>GRangesList</i>.</p

Figure 6

<p>Top panels: distributions of alternate nucleotide proportions for on- and off-SNP allele-dependent CTCF binding events. Bottom panels: relationships between average call quality values and alternate nucleotide proportions are depicted using a 2D density estimate (darker regions correspond to higher density.).</p

Illustration of the reduce and disjoin operations on the last exon from each of the <i>KRAS</i> transcripts.

<p>Illustration of the reduce and disjoin operations on the last exon from each of the <i>KRAS</i> transcripts.</p

Ranges for the first three reads in the ctcfReads object, storing the read alignments for the CTCF sample.

<p>Ranges for the first three reads in the ctcfReads object, storing the read alignments for the CTCF sample.</p

Contents of the krasA object, representing the exons in isoform A of KRAS.

<p>Contents of the krasA object, representing the exons in isoform A of KRAS.</p

Selected packages based on the Ranges infrastructure.

<p>Categories are biocViews terms. Up to 4 packages were randomly sampled from Bioconductor packages that explicitly declare a dependence on <i>IRanges</i>, <i>GenomicRanges</i>, or <i>GenomicFeatures</i> packages.</p

Illustration of overlap computations between two <i>GRangesList</i> objects.

<p>Each set of rectangles linked by solid lines represents a compound range, i.e., an element of the list. Ranges in the query (top) are being matched against ranges in the subject (bottom). The labels between them indicate the type of overlap (any, within, none).</p

Tabular (top) and visual (bottom) representation of the exons for the human <i>KRAS</i> gene, derived from the UCSC known gene annotation.

<p>In the table, the columns <i>seqnames</i>, <i>start</i> and <i>end</i> locate the exons in the genome. The <i>strand</i> column indicates the direction of transcription. The exons are grouped into transcripts by <i>tx_id</i>, and the exon IDs are given by <i>exon_id</i>. Virtually all genomic data sets fit this pattern: genomic location, followed by a series of columns, often including strand and/or score, that annotate that location. In the plot, the rectangles represent exonic regions, and the arrows represent the introns, as well as the strand.</p

Visualization of the coverage of bases by GFP- and CTCF-bound fragments (top) in the context of part of the gene model for Rrp1, Entrez gene 18114 (bottom).

<p>Visualization of the coverage of bases by GFP- and CTCF-bound fragments (top) in the context of part of the gene model for Rrp1, Entrez gene 18114 (bottom).</p