compare {Onassis}R Documentation

compare

Description

This method compares a list of scored entities according to the semantic annotations of this entities in the semantic sets defined by a single ontology or, in case of annotations with two ontologies, the difference between second level semantic sets within a give first level semantic set (e.g. different diseases within a given tissue)

Usage

compare(onassis, ...)

## S4 method for signature 'Onassis'
compare(onassis, score_matrix = NA, by = "row",
  fun_name = "wilcox.test")

Arguments

onassis

instance of class Onassis-class

...

Optional parameters

score_matrix

a matrix of scores containing on the rows genomic units and on the columns the samples annotated in the entities

by

'row' if the test refers to single genomic units in multiple conditions, 'col' if the test compares all the genomic units across different conditions

fun_name

name of the test to apply

Value

The results of the comparison between semantic classes

Examples

geo_chip <- readRDS(system.file('extdata', 'vignette_data','GEO_human_chip.rds', package='Onassis'))
geo_chip <- geo_chip[sample(nrow(geo_chip), 30) ,]
obo1 <- system.file('extdata', 'sample.cs.obo', package='OnassisJavaLibs')
obo2 <- system.file('extdata', 'sample.do.obo', package='OnassisJavaLibs')
onassis_results1 <- annotate(geo_chip, 'OBO', dictionary=obo1)
onassis_results2 <- annotate(geo_chip, 'OBO', dictionary=obo2)
n <- length(unique(geo_chip$sample_accession))
m <- 50
score_matrix <-   matrix(sample(0:1, m * n, replace = TRUE), m, n)
colnames(score_matrix) <- unique(geo_chip$sample_accession)
rownames(score_matrix) <- paste0('gene_', seq(1, m, 1))
my_onassis <- mergeonassis(onassis1 = onassis_results1, onassis2 = onassis_results2)
scores(my_onassis) <- score_matrix

comparisons <- compare(my_onassis)
comparisons2 <- compare(my_onassis, by='col', fun_name='kruskal.test')
scores(onassis_results1) <- score_matrix
comparisons3 <- compare(onassis_results1)
comparisons4 <- compare(onassis_results1, by='col', fun_name='kruskal.test')

[Package Onassis version 1.2.7 Index]