00-datasets: SVAlignR Sample Data

In SVAlignR: Recovering Structure of Long Molecules from Structural Variation Data

SVAlignR Sample Data

Description

These data sets contain binary versions of data describing breakpoints and long read sequences from an HPV-positive head-and-neck cancer sample.

Usage

data("longreads")

Format

longreads

A data frame with 197 rows and 5 columns. Each row represents a single Oxford Nanopore long read from a study of a cell line from an HPV-positive head-and-neck squamous cell tumor. The five columns contain (i) a unique identifier of each long read, (ii) the length of the read, in bytes, (iii) the ordered sequence of break points, represented as a hyphen separated list of numeric identifiers, (iv) manually estimated natural groups of reads, and (v) a manually curated indication of whether certain long reads should be omitted from the analysis.

breakpoints

A data frame with 82 rows and 11 columns. Each row represents a single breakpoint from a study of a cell line from an HPV-positive head-and-neck squamous cell tumor. The columns contain (1) a unique identifier that is used in the long read connections, (2-4) a description of the chromosomal segment to the left of the breakpoint, (5-7) a description of the chromosomal segment to the right of the breakpoint, (8-9) the orientation of the two chromosomal segments, (10) a shorthand description of the breakpoint with the segment names separated by a vertical bar and negative strands contained in parentheses, and (11) a shorthand representation of the reverse orientation of the breakpoint.

Author(s)

Kevin R. Coombes <[e-mail]>

Source

Long read (Oxford Nanopore) sequencing was performed on samples prepared at the laboratory of Maura Gillison and David Symer. Characterization of long reads as a sequence of well-defined break points was performed by Keiko Akagi.

Examples

data(longreads)
head(longreads)

alphabet <- Cipher(longreads$connection)
en <- encode(alphabet, "0-50-74-0-50-74-35")
en
decode(alphabet, en)

SVAlignR documentation built on Sept. 4, 2025, 3:01 p.m.