compareTaxonGroups: Compare the score distributions between 2 taxon groups

In BIONF/PhyloProfile: PhyloProfile

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 ([e-mail])

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 Dec. 18, 2024, 7:33 a.m.