comparison: Comparison class and class functions

In genoPlotR: Plot Publication-Grade Gene and Genome Maps

Description

A comparison is a collection of similarities, representing the comparison 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	Can be a list or data.frame object. See the details for the columns in the data.frame.
df	A data.frame object. See details for the required columns.
comparison	Any object to test.

Details

Objects (either data frames or lists) should have at least named elements start1, end1, start2 and end2. In addition, it can take a color column. Additional numeric columns can be used for color-coding (via apply_color_scheme.

comparison tries to build a comparison object from either a data frame or a list, as.comparison accepts only data.frames.

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

Read functions such as read_comparison_from_tab and read_comparison_from_blast also return comparison objects.

Value

A comparison object for comparison and as.comparison. Comparison objects are also of class data.frame. They contain the columns start1, end1, start2, end2, direction and col (color).

A logical for is.comparison.

Author(s)

Lionel Guy

See Also

dna_seg, read_comparison_from_tab, read_comparison_from_blast, trim.comparison, reverse.comparison.

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))
comparison1
is.comparison(comparison1)
is.data.frame(comparison1)
comparison(data.frame(start1=starts1, end1=ends1,
                      start2=starts2, end2=ends2))
## From a list
comparison(list(start1=starts1, end1=ends1,
                start2=starts2, end2=ends2))

## From a file
comparison2_file <- system.file('extdata/comparison2.tab',
                                package = 'genoPlotR')
comparison2 <- read_comparison_from_tab(comparison2_file)

genoPlotR documentation built on Jan. 5, 2021, 3:02 p.m.