TOY24_focalgenome: 'focalgenome' example for 24 markers, created for...

In dorolin/rearrvisr: Detect, Classify, and Visualize Genome Rearrangements

Description

A data set illustrating a focal (extant) genome map with 24 markers on three genome segments (e.g., scaffolds).

Usage

TOY24_focalgenome

Format

A data frame with markers in rows and five columns that specify the structure of a focal genome map:

$marker	unique ortholog ID of marker
$scaff	genome segment where marker is located
$start	start position of marker on genome segment
$end	end position of marker on genome segment
$strand	reading direction of marker

See Also

computeRearrs, TOY24_compgenome

Examples

## Not run: 

## recreate the data set
TOY24_focalgenome <- data.frame(
  marker = as.integer(c(1,7,2,6:4,8:10,3,13:11,14,17:15,18,21,20,22:24,19)),
  scaff = as.character(rep(c(1,2,3), times = c(7,11,6))),
  start = as.integer(c(seq(10^6, by = 10^6, length.out = 7),
                       seq(10^6, by = 10^6, length.out = 11),
                       seq(10^6, by = 10^6, length.out = 6))),
  end = as.integer(c(seq(10^6+2, by = 10^6, length.out = 7),
                     seq(10^6+2, by = 10^6, length.out = 11),
                     seq(10^6+2, by = 10^6, length.out = 6))),
  strand = rep(rep(c("+", "-"), 4),
               times = c(4,2,4,3,8,1,1,1)),
  stringsAsFactors = FALSE)

## End(Not run)

dorolin/rearrvisr documentation built on Aug. 6, 2020, 1:32 a.m.