recalculateScore: The output of fdogFAS is a phylogenetic profile (pp). But...
In giangnguyen0709/fCAT: fCAT

Description Usage Arguments Value Examples

The output of fdogFAS is a phylogenetic profile (pp). But this pp still can not be used to assess the completeneness of the interested genome. The pp will contains the ortholog sequence within the training sequence. The FAS score of each sequence is the FAS score between itself and the core group's ortholog sequence. Therefore the score must be recalculated, for score mode 2 and 3 the score between the ortholog sequence and the score of the training sequence must be swaped. For score mode 1 the avarage score of the training sequences must be calculated and updated into the line of the ortholog sequence. This function will be used as a modul in concanateFiles. The function will remove all the line of the training sequences and return the pp of the interested genome.

1	recalculateScore(pp, genomeName)

`pp`	The phylogenetic profile output from fdogFAS in form of a data.frame
`genomeName`	The genome ID of the interested genome

The phylogenetic profile of the interested genome.

## Create pseudo phylogenetic profile data
geneID <- c(
    "1426075at2759", "1426075at2759", "1426075at2759", "1426075at2759"
)
ncbiID <- c("ncbi9606", "ncbi3055", "ncbi3702", "ncbi400682")
orthoID <- c(
    "1426075at2759|HUMAN@9606@3|P0DI81|0",
    "1426075at2759|CHLRE@3055@2|3055_0:003348|1",
    "1426075at2759|ARATH@3702@2|3702_0:00057f|1",
    "1426075at2759|AMPQU@400682@2|400682_0:000143|1"
)
FAS_F <- c(1, 0.99766, 0.9975999, 0.996729)
FAS_B <- c(1, 0.99766, 0.99759, 0.996729)
pp <- data.frame(geneID, ncbiID, orthoID, FAS_F, FAS_B)

## recalculating scores
rePP <- recalculateScore(pp, "HUMAN@9606@3")
print.data.frame(rePP)