translateReport: Translate the report table into a frequence table, which tell...

In giangnguyen0709/fCAT: fCAT

Description

Translate the report table into a frequence table, which tell the user, how many "dissimilar", "simillar", "missing", etc.

Usage

translateReport(genomeID, report, scoreMode)

Arguments

genomeID	the genome ID of the interested genome
report	the report of the completeness of the interested genome based on its phylogenetic profile
scoreMode	the mode determines the method to scoring the founded ortholog and how to classify them. Choices: 1, 2, 3, "busco"

Value

A frequency table of the completeness of the interested genome in data.frame

Examples

## Create a pseudo phylogenetic profile table
geneID <- c("530670", "530730")
ncbiID <- c("ncbi9606", "ncbi9606")
orthoID <- c("530670|HUMAN@9606@3|Q16526|1", "530730|HUMAN@9606@3|P05091|1")
FAS_F <- c(1, 1)
FAS_B <- c(1, 1)
pp <- data.frame(geneID, ncbiID, orthoID, FAS_F, FAS_B)
coreFolder <- system.file("extdata", "sample", package = "fCAT")
## Translate phylogenetic profile to a detailed report
report <- reportSingle(pp, coreFolder, "test", 2, c("HUMAN@9606@1"))
## Translate the report table to a frequency table
frequencyTable <- translateReport("HUMAN@9606@3", report, 2)
print.data.frame(frequencyTable)

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