compareTaxonGroups {PhyloProfile} | R Documentation

## Compare the score distributions between 2 taxon groups

### Description

Given the phylogenetic profiles that contains up to 2 additional variables besides the presence/absence information of the orthologous proteins. This function will compare the distribution of those variables between 2 different taxon groups (e.g. parasitic species vs non-parasitic species), which are defined as in-group and out-group. In-group is identified by the user. Out-group contains all taxa in the input phylogenetic profiles that are not part of the in-group.

### Usage

    compareTaxonGroups(data, inGroup, useCommonAncestor, variable,
        significanceLevel)

### Arguments

`data` | input phylogenetic profile in long format (see ?mainLongRaw and ?createLongMatrix)
`inGroup` | ID list of in-group taxa (e.g. "ncbi1234")
`useCommonAncestor` | TRUE/FALSE if using all taxa that share the same common ancestor with the pre-selected in-group as the in-group taxa. Default = TRUE.
`variable` | name of the variable that need to be compared
`significanceLevel` | significant cutoff for the statistic test (between 0 and 1). Default = 0.05.

### Value

list of genes that have a significant difference in the variable distributions between the in-group and out-group taxa and their corresponding p-values.

### Author(s)

Vinh Tran (tran@bio.uni-frankfurt.de)

### Examples

    data("mainLongRaw", package="PhyloProfile")
    data <- mainLongRaw
    inGroup <- c("ncbi9606", "ncbi10116")
    variable <- colnames(data)[4]
    compareTaxonGroups(data, inGroup, TRUE, variable, 0.05)

[Package PhyloProfile version 1.4.11 Index]