experiment_similarity {SkeletalVis} | R Documentation |
Get cosine similarity for a query dataset against the skeletalvis database
Description
Computes the cosine similarity of the log2 fold changes of a given query dataset against the SkeletalVis fold changes, returning a data frame of experiment similarities.
Usage
experiment_similarity(skeletalvis, dataset, add_meta_data = TRUE)
Arguments
skeletalvis |
The path to the SkeletalVis data folder. |
dataset |
A dataframe with human gene symbols and log2 fold changes. |
add_meta_data |
Add metadata such as species, tissue, description of overall experiment and specific comparison |
Value
A data frame containing cosine similarity values, IDs, and z-scores.
Examples
skeletalvis <- load_skeletalvis(demo=TRUE)
# Create a query dataset (this should be a data frame with the first column as gene IDs)
query_dataset <- data.frame(ID = c("SOX9", "ACAN"), fold_change = c(2.5, -1.8))
# Get cosine similarities
similarity_results <- experiment_similarity(
skeletalvis = skeletalvis,
dataset = query_dataset,
)
# View results
head(similarity_results)
[Package SkeletalVis version 0.1.1 Index]