README.md
In gzentner/ZentUtils: Miscellaneous Tools for Sequence Analysis

About

ZentUtils is a collection of functions designed to streamline analysis of genomic intervals.

What does it do?

Region sorting by coordinate or score
Region expansion
Retrieval of region sequences
Plotting of region sequences as a color map

Example: plotting sequences around motif matches

Included with ZentUtils is a BED file of matches to motifs for the yeast Reb1 transcription factor.

Import regions into ZentUtils

First, a 6-column BED file is imported into ZentUtils and converted to a GRanges object that is stored in the regions slot of a new ZentUtils object.

zent <- zentutils(system.file("extdata", "homer_reb1_badis_motif_scan.bed", package = "ZentUtils"), genome = "sacCer3")

Sort regions

Next, we sort the regions. Regions can be sorted by coordinate with by = "coord" or by score (5th column of the BED file) with by = "score".

zent <- sort_regions(zent, by = "score", decreasing = TRUE)

Expand regions

We then optionally expand the regions of interest to a specified size. For expansion, length bases are added to both ends of each region. Expanded regions are stored in the expanded_regions slot of the ZentUtils object. Sequences that are out-of-bounds following expansion are discarded.

zent <- expand_regions(zent, length = 10)

Retrieve region sequences

Sequences for the imported or expanded regions are then obtained from a BSgenome object and stored in the seqs slot of the ZentUtils object.

genome <- BSgenome.Scerevisiae.UCSC.sacCer3
zent <- get_seqs(zent, region_type = "expanded", genome = genome)

Generate sequence color map

Lastly, we generate a tile plot, wherein each base is represented by a specific color. This allows efficient visual detection of specific sequences patterns around features of interest.