extractPP: This function takes a phylogenetic profile, which contains...

In giangnguyen0709/fCAT: fCAT

Description

This function takes a phylogenetic profile, which contains many different genomes as an input and extract the phylogenetic profile of a specific genome

Usage

extractPP(pp, genome)

Arguments

pp	A phylogenetic profile in data.frame
genome	The genome ID of the genome, whose pp need to be extracted. Exp: genome = HUMAN@9606@3

Value

The phylogenetic profile of the interested genome in data.frame

Examples

## Create pseudo phylogenetic profile, which contains two different genomes
geneID <- c("530670", "530730", "603043")
ncbiID <- c("ncbi9606", "ncbi9606", "ncbi9606")
orthoID <- c(
    "530670|HUMAN@9606@3|Q16526|1", "530730|HUMAN@9606@3|P05091|1",
    "603043|HOMSA@9606@2|Q39233|1"
)
FAS_F <- c(1, 1, 1)
FAS_B <- c(1, 1, 1)
pp <- data.frame(geneID, ncbiID, orthoID, FAS_F, FAS_B)
newPP <- extractPP(pp, "HUMAN@9606@3")
print.data.frame(newPP)

giangnguyen0709/fCAT documentation built on Feb. 10, 2021, 4:31 a.m.