| filterProfileData {PhyloProfile} | R Documentation |
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!
filterProfileData(DF, refTaxon = NULL,
percentCO = c(0, 1), coorthoCOMax = 9999,
var1CO = c(0, 1), var2CO = c(0, 1), var1Rel = "protein",
var2Rel = "protein", groupByCat = FALSE, catDt = NULL)
DF |
a reduced dataframe contains info for all phylogenetic profiles in the selected taxonomy rank. |
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. |
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).
Vinh Tran tran@bio.uni-frankfurt.de
parseInfoProfile and reduceProfile
for generating input dataframe, fullProcessedProfile for a
demo full processed profile dataframe, fromInputToProfile for
generating fully processed data from raw input.
# 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")
superTaxonDf <- reduceProfile(fullProcessedProfile)
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
filterProfileData(
superTaxonDf,
refTaxon,
percentCutoff,
coorthologCutoffMax,
var1Cutoff,
var2Cutoff,
var1Relation,
var2Relation,
groupByCat,
catDt
)