as.data.frame: Convert results to Data Frame

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

Convert results to Data Frame

Description

Convert return of functions in sitePath package to a data.frame so can be better worked with. The group name for each tip is the same as groupTips.

A fixationSites object will output the mutation name of the fixation and the cluster name before and after the mutation.

An SNPsites object will output the tip name with the SNP and its position.

An parallelSites object will output the tip name with the group name and mutation info.

Usage

## S3 method for class 'fixationSites'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S3 method for class 'SNPsites'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

## S3 method for class 'parallelSites'
as.data.frame(x, row.names = NULL, optional = FALSE, ...)

Arguments

x	The object to be converted to data.frame.
row.names	Unimplemented.
optional	Unimplemented.
...	Other arguments.

Value

A data.frame object.

Examples

data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
fixations <- fixationSites(lineagePath(tree))
as.data.frame(fixations)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.