comparison class and methods

comparison objects are collections of similarities between two DNA segments. These functions are class functions to create, convert, and test comparison objects.

Usage

comparison(x)

as.comparison(df)

is.comparison(comparison)

Arguments

x: An object to be coerced. Can be a list, data.frame or data.table object. See details for necessary columns.
df: Same as x.
comparison: An object to test.

Value

as.comparison and comparison both return a comparison object.

is.comparison returns a logical.

Details

A comparison object requires at least the start1, end1, start2, and end2 columns. A color can be provided as well using the col column. Additional numeric columns can be used for color-coding using [gradient_color_scheme], or the "gradient" color scheme in the global_color_scheme argument in [plot_gene_map].

These objects inherit from data.table, and can therefore be manipulated using data.table syntax.

is.comparison returns TRUE if the object tested is a comparison object.

Author

Lionel Guy

Examples

## Get some values
starts1 <- c(2, 1000, 1050)
ends1 <- c(600, 800, 1345)
starts2 <- c(50, 800, 1200)
ends2 <- c(900, 1100, 1322)

## From a data.frame
comparison1 <- as.comparison(data.frame(start1 = starts1, end1 = ends1,
                                        start2 = starts2, end2 = ends2))
print_comparison(comparison1)
#>    start1  end1 start2  end2 direction
#>     <num> <num>  <num> <num>     <num>
#> 1:      2   600     50   900         1
#> 2:   1000   800    800  1100        -1
#> 3:   1050  1345   1200  1322         1
is.comparison(comparison1)
#> [1] TRUE
is.data.frame(comparison1)
#> [1] TRUE
print_comparison(data.frame(start1 = starts1, end1 = ends1,
                            start2 = starts2, end2 = ends2))
#>    start1  end1 start2  end2
#>     <num> <num>  <num> <num>
#> 1:      2   600     50   900
#> 2:   1000   800    800  1100
#> 3:   1050  1345   1200  1322

## From a list
print_comparison(list(start1 = starts1, end1 = ends1,
                      start2 = starts2, end2 = ends2))
#>    start1  end1 start2  end2
#>     <num> <num>  <num> <num>
#> 1:      2   600     50   900
#> 2:   1000   800    800  1100
#> 3:   1050  1345   1200  1322


## Printing out a comparison like this can occasionally throw an error:
if (FALSE) { # \dontrun{
comparison1
print(comparison1)
} # }
## This can happen when print.comparison is loaded from the testthat package
## To avoid this, use print_comparison as shown above