as.data.frame.fixationSites {sitePath} | R Documentation

## 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)

[Package sitePath version 1.6.6 Index]