SkeletalVis (version 0.1.2)

experiment_similarity: 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)

Value

A data frame containing cosine similarity values, IDs, and z-scores.

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

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)