parseInfoProfile {PhyloProfile} | R Documentation

## Parsing info for phylogenetic profiles

### Description

Creating main dataframe for the input phylogenetic profiles based on selected input taxonomy level (e.g. strain, species) and reference taxon. The output contains the number of paralogs, the max/min/mean/median of VAR1 and VAR2.

### Usage

    parseInfoProfile(inputDf, sortedInputTaxa, taxaCount, coorthoCOMax)

### Arguments

`inputDf` | input profiles in long format
`sortedInputTaxa` | sorted taxonomy data for the input taxa (check sortInputTaxa())
`taxaCount` | dataframe counting present taxa in each supertaxon
`coorthoCOMax` | maximum number of co-orthologs allowed

### Value

A dataframe contains all info for the input phylogenetic profiles. This full processed profile that is required for several profiling analyses e.g. estimation of gene age (?estimateGeneAge) or identification of core gene (?getCoreGene).

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`createLongMatrix`, `sortInputTaxa`, `calcPresSpec`, `mainLongRaw`

### Examples

    data("mainLongRaw", package="PhyloProfile")
    taxonIDs <- getInputTaxaID(mainLongRaw)
    sortedInputTaxa <- sortInputTaxa(
        taxonIDs, "class", "Mammalia", NULL
    )
    taxaCount <- plyr::count(sortedInputTaxa, "supertaxon")
    coorthoCOMax <- 999
    parseInfoProfile(
        mainLongRaw, sortedInputTaxa, taxaCount, coorthoCOMax
    )

[Package PhyloProfile version 1.4.11 Index]