compare {Onassis} | R Documentation |
compare
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)
compare(onassis, ...) ## S4 method for signature 'Onassis' compare(onassis, score_matrix = NA, by = "row", fun_name = "wilcox.test")
onassis |
instance of 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 |
The results of the comparison between semantic classes
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')