filterProfileData {PhyloProfile} | R Documentation

## Filter phylogentic profiles

### Description

Create a filtered data needed for plotting or clustering phylogenetic profiles. NOTE: this function require some intermediate steps using the results from other functions. If you would like to get a full processed data from the raw input, please use the function fromInputToProfile() instead!

### Usage

    filterProfileData(DF, taxaCount, refTaxon = NULL,
        percentCO = c(0, 1), coorthoCOMax = 9999,
        var1CO  = c(0, 1), var2CO = c(0, 1), var1Rel = "protein",
        var2Rel = "protein", groupByCat = FALSE, catDt = NULL,
        var1AggregateBy = "max", var2AggregateBy = "max")

### Arguments

`DF` | a reduced dataframe contains info for all phylogenetic profiles in the selected taxonomy rank.
`taxaCount` | dataframe counting present taxa in each supertaxon
`refTaxon` | selected reference taxon. NOTE: This taxon will not be affected by the filtering. If you want to filter all, set refTaxon <- NULL. Default = NULL.
`percentCO` | min and max cutoffs for percentage of species present in a supertaxon. Default = c(0, 1).
`coorthoCOMax` | maximum number of co-orthologs allowed. Default = 9999.
`var1CO` | min and max cutoffs for var1. Default = c(0, 1).
`var2CO` | min anc max cutoffs for var2. Default = c(0, 1).
`var1Rel` | relation of var1 ("protein" for protein-protein or "species" for protein-species). Default = "protein".
`var2Rel` | 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 (optional, NULL if groupByCat = FALSE or no info provided). Default = NULL.
`var1AggregateBy` | aggregate method for VAR1 (max, min, mean or median), applied for calculating var1 of supertaxa. Default = "max".
`var2AggregateBy` | aggregate method for VAR2 (max, min, mean or median), applied for calculating var2 of supertaxa. Default = "max".

### Value

A filtered dataframe for generating profile plot including 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, supertaxon, and the categories of seed genes (or ortholog groups).

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`parseInfoProfile` and `reduceProfile` for generating input dataframe, `fullProcessedProfile` for a demo full processed profile dataframe, `fromInputToProfile` for generating fully processed data from raw input.

### Examples

    # NOTE: this function require some intermediate steps using the results from
    # other functions. If you would like to get a full processed data from the
    # raw input, please use the function fromInputToProfile() instead!
    data("fullProcessedProfile", package="PhyloProfile")
    rankName <- "class"
    refTaxon <- "Mammalia"
    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
    var1AggregateBy <- "max"
    var2AggregateBy <- "max"
    taxonIDs <- levels(as.factor(fullProcessedProfile$ncbiID))
    sortedInputTaxa <- sortInputTaxa(
        taxonIDs, rankName, refTaxon, NULL
    )
    taxaCount <- plyr::count(sortedInputTaxa, "supertaxon")
    filterProfileData(
        fullProcessedProfile,
        taxaCount,
        refTaxon,
        percentCutoff,
        coorthologCutoffMax,
        var1Cutoff,
        var2Cutoff,
        var1Relation,
        var2Relation,
        groupByCat,
        catDt,
        var1AggregateBy,
        var2AggregateBy
    )

[Package PhyloProfile version 1.4.11 Index]