PhyloProfile: PhyloProfile

linearizeArchitecture

R Documentation

Linearize PFAM/SMART annotations by best e-value/bitscore

Description

Linearize PFAM/SMART annotations by best e-value/bitscore

Usage

linearizeArchitecture(domainDf = NULL, orthoID = NULL, value = "evalue")

Arguments

`domainDf`	input domain dataframe
`orthoID`	ID of protein that needs to be linearized
`value`	type of values that will be used for linearized, either evalue (default) or bitscore

Value

Domain dataframe of the selected protein after linearization

Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

Examples

demoDomainDf <- data.frame(
    orthoID = rep("protID", 4),
    start = c(1, 5, 100, 80),
    end = c(30, 40, 130, 110),
    evalue = c(0.001, 0.0005, 0.2, 0.004),
    feature_type = c(rep("pfam", 2), rep("smart", 2)),
    feature_id = c("pf1", "pf2", "sm1", "sm2")
)
linearizeArchitecture(demoDomainDf, "protID", "evalue")

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.