Fetch data from Malaria Cell Atlas — easyMCA • plasmoRUtils

This function fetches and loads the metadata and expression matrices from the desired data sets available on Malaria Cell Atlas (MCA) Database.

Usage

easyMCA(url, type = "data")

Arguments

url: A url of dataset from listMCA function.
type: Type of data to be fetched. Use "exp" to fetch normalized and scaled values, use "raw" to get raw counts and use "data" to get the metadata of the dataset.

Value

df A dataframe of requested data type from MCA.

Examples

if (FALSE) { # \dontrun{
  url <- "https://www.malariacellatlas.org/downloads/pf-ch10x-set4-biorxiv.zip"
  # Use the function to read metadata, expression, or raw data
  metadata <- easyMCA(url, type = "data")
  expression <- easyMCA(url, type = "exp")
  raw_counts <- easyMCA(url, type = "raw")

  ## make Seurat Object easily now

  testmca <- Seurat::CreateSeuratObject(counts = raw_counts, meta.data = metadata, project = "MCA")
} # }