Nothing
## ----echo=FALSE---------------------------------------------------------------
knitr::opts_chunk$set(fig.width=7, fig.height=7)
## -----------------------------------------------------------------------------
library(ontologyIndex)
library(ontologySimilarity)
library(SimReg)
data(hpo)
set.seed(1)
terms <- get_ancestors(hpo, c(hpo$id[match(c("Abnormality of thrombocytes","Hearing abnormality"),
hpo$name)], sample(hpo$id, size=50)))
## -----------------------------------------------------------------------------
hearing_abnormality <- hpo$id[match("Hearing abnormality", hpo$name)]
genotypes <- c(rep(TRUE, 2), rep(FALSE, 98))
#give all subjects 5 random terms and add 'hearing abnormality' for those with y_i=TRUE
phenotypes <- lapply(genotypes, function(y_i) minimal_set(hpo, c(
if (y_i) hearing_abnormality else character(0), sample(terms, size=5))))
## -----------------------------------------------------------------------------
sim_reg(ontology=hpo, x=phenotypes, y=genotypes)
## -----------------------------------------------------------------------------
term_weights <- ifelse(grepl(x=hpo$name, ignore=TRUE, pattern="hearing"), 10, 1)
names(term_weights) <- hpo$id
## -----------------------------------------------------------------------------
thrombocytes <- hpo$id[match("Abnormality of thrombocytes", hpo$name)]
literature_phenotype <- c(hearing_abnormality, thrombocytes)
info <- get_term_info_content(hpo, phenotypes)
term_weights_resnik <- apply(get_term_set_to_term_sims(
ontology=hpo, information_content=info, terms=names(info),
term_sim_method="resnik", term_sets=list(literature_phenotype)), 2, mean)
## -----------------------------------------------------------------------------
sim_reg(
ontology=hpo,
x=phenotypes,
y=genotypes,
term_weights=term_weights_resnik
)
## ----eval=FALSE---------------------------------------------------------------
# annotation_df <- read.table(header=FALSE, skip=1, sep="\t",
# file="ALL_SOURCES_TYPICAL_FEATURES_genes_to_phenotype.txt", stringsAsFactors=FALSE, quote="")
# hpo_by_gene <- lapply(split(f=annotation_df[,2], x=annotation_df[,4]),
# function(trms) minimal_set(hpo, intersect(trms, hpo$id)))
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