dataFeatureTaxGroup {PhyloProfile} | R Documentation

## 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 (tran@bio.uni-frankfurt.de)

### 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)

[Package PhyloProfile version 1.4.11 Index]