dataFeatureTaxGroup: Create data for feature distribution comparison plot

In BIONF/PhyloProfile: PhyloProfile

Create data for feature distribution comparison plot

Description

Create data for plotting the distribution of the protein domain features between 2 group of taxa for a selected gene (average number of feature occurrency per protein/ortholog).

Usage

dataFeatureTaxGroup(mainDf, domainDf, inGroup, gene)

Arguments

mainDf	input phylogenetic profile in long format (see ?mainLongRaw and ?createLongMatrix)
domainDf	dataframe contains domain info for the seed and ortholog. This including the seed ID, orthologs IDs, sequence lengths, feature names, start and end positions, feature weights (optional) and the status to determine if that feature is important for comparison the architecture between 2 proteins* (e.g. seed protein vs ortholog) (optional). (see ?parseDomainInput)
inGroup	ID list of in-group taxa (e.g. "ncbi1234")
gene	ID of gene that need to be plotted the feature distribution comparison between in- and out-group taxa.

Value

Dataframe containing all feature names, their frequencies (absolute count and the average instances per protein - IPP) in each taxon group and the corresponding taxa group type (in- or out-group).

Author(s)

Vinh Tran ([e-mail])

See Also

createLongMatrix, parseDomainInput

Examples

data("mainLongRaw", package="PhyloProfile")
mainDf <- mainLongRaw
gene <- "101621at6656"
inputFile <- system.file(
    "extdata", "domainFiles/101621at6656.domains",
    package = "PhyloProfile", mustWork = TRUE
)
type <- "file"
domainDf <- parseDomainInput(gene, inputFile, type)
inGroup <- c("ncbi9606", "ncbi10116")
dataFeatureTaxGroup(mainDf, domainDf, inGroup, gene)

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