compareTaxonGroups: Compare the score distributions between 2 taxon groups

View source: R/compareTaxaGroups.R

compareTaxonGroupsR 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, taxDB)

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.

taxDB

Path to the taxonomy DB files

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)

BIONF/PhyloProfile documentation built on March 29, 2024, 5:26 a.m.