genoPlotR (version 0.8.11)

comparison: Comparison class and class functions

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.

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.

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.

See Also

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

Examples

# NOT RUN {
## 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)

# }