fromInputToProfile: Complete processing of raw input phylogenetic profiles

In BIONF/PhyloProfile: PhyloProfile

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, sortedTaxonList = 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, taxDB = 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.
sortedTaxonList	list of sorted taxa (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
taxDB	Path to the taxonomy DB files

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 [e-mail]

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
sortedTaxonList <- 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,
    sortedTaxonList,
    var1AggregateBy,
    var2AggregateBy,
    percentCutoff,
    coorthologCutoffMax,
    var1Cutoff,
    var2Cutoff,
    var1Relation,
    var2Relation,
    groupByCat,
    catDt
)

BIONF/PhyloProfile documentation built on Nov. 7, 2024, 8:31 p.m.