fromInputToProfile {PhyloProfile} | R Documentation

## Complete processing of raw input phylogenetic profiles

### Description

Create a processed and filtered data for plotting or analysing phylogenetic profiles from raw input file (from raw input to final filtered dataframe)

### Usage

    fromInputToProfile(rawInput, rankName, refTaxon = NULL,
        taxaTree = NULL, var1AggregateBy = "max", var2AggregateBy = "max",
        percentCutoff = c(0, 1), coorthologCutoffMax = 9999,
        var1Cutoff = c(0, 1), var2Cutoff = c(0, 1), var1Relation = "protein",
        var2Relation = "protein", groupByCat = FALSE, catDt = NULL)

### Arguments

`rawInput` | input file (in long, wide, multi-fasta or orthoxml format)
`rankName` | taxonomy rank (e.g. "species","phylum",...)
`refTaxon` | selected reference taxon name (used for sorting and will be protected from filtering). Default = NULL.
`taxaTree` | input taxonomy tree for taxa in input profiles (optional). Default = NULL.
`var1AggregateBy` | aggregate method for var1 (min, max, mean or median). Default = "max".
`var2AggregateBy` | aggregate method for VAR2 (min, max, mean or median). Default = "max".
`percentCutoff` | min and max cutoffs for percentage of species present in a supertaxon. Default = c(0, 1).
`coorthologCutoffMax` | maximum number of co-orthologs allowed. Default = 9999.
`var1Cutoff` | min and max cutoffs for var1. Default = c(0, 1).
`var2Cutoff` | min and max cutoffs for var2. Default = c(0, 1).
`var1Relation` | relation of var1 ("protein" for protein-protein or "species" for protein-species). Default = "protein".
`var2Relation` | relation of var2 ("protein" for protein-protein or "species" for protein-species). Default = "protein".
`groupByCat` | group genes by their categories (TRUE or FALSE). Default = FALSE.
`catDt` | dataframe contains gene categories. Default = NULL.

### Value

Dataframe required for generating phylogenetic profile plot or clustering analysis. It contains seed gene IDs (or orthologous group IDs), their ortholog IDs and the corresponding (super)taxa, (super)taxon IDs, number of co-orthologs in each (super)taxon, values for two additional variables var1, var2, categories of seed genes (or ortholog groups).

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`createLongMatrix`, `getInputTaxaID`, `getInputTaxaName`, `sortInputTaxa`, `parseInfoProfile`, `reduceProfile`, `filterProfileData`

### Examples

    rawInput <- system.file(
        "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
    )
    rankName <- "class"
    refTaxon <- "Mammalia"
    taxaTree <- NULL
    var1AggregateBy <- "max"
    var2AggregateBy <- "mean"
    percentCutoff <- c(0.0, 1.0)
    coorthologCutoffMax <- 10
    var1Cutoff <- c(0.75, 1.0)
    var2Cutoff <- c(0.5, 1.0)
    var1Relation <- "protein"
    var2Relation <- "species"
    groupByCat <- FALSE
    catDt <- NULL
    fromInputToProfile(
        rawInput,
        rankName,
        refTaxon,
        taxaTree,
        var1AggregateBy,
        var2AggregateBy,
        percentCutoff,
        coorthologCutoffMax,
        var1Cutoff,
        var2Cutoff,
        var1Relation,
        var2Relation,
        groupByCat,
        catDt
    )

[Package PhyloProfile version 1.4.11 Index]