In rnabioco/clustifyrdatahub: External data sets for clustifyr in ExperimentHub

knitr::opts_chunk$set(
  collapse = TRUE,
  message = FALSE,
  warning = FALSE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

clustifyrdatahub

clustifyrdatahub provides external reference data sets for cell-type assignment with clustifyr.

Installation

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("clustifyrdatahub")

Available references include

knitr::kable(dplyr::select(
  read.csv(system.file("extdata", "metadata.csv", package = "clustifyrdatahub")),
  c(1, 9, 2:7)))

To use clustifyrdatahub

library(ExperimentHub)
eh <- ExperimentHub()

## query
refs <- query(eh, "clustifyrdatahub")
refs
## either by index or id
ref_hema_microarray <- refs[[7]]         ## load the first resource in the list
ref_hema_microarray <- refs[["EH3450"]]  ## load by EH id

## or list and load
refs <- listResources(eh, "clustifyrdatahub")
ref_hema_microarray <- loadResources(eh, "clustifyrdatahub", "ref_hema_microarray")[[1]]

## use for classification of cell types
res <- clustifyr::clustify(
  input = clustifyr::pbmc_matrix_small,
  metadata = clustifyr::pbmc_meta$classified,
  ref_mat = ref_hema_microarray,
  query_genes = clustifyr::pbmc_vargenes
)

## or load refs by function name (after loading hub library)
library(clustifyrdatahub)
ref_hema_microarray()[1:5, 1:5]           ## data are loaded
ref_hema_microarray(metadata = TRUE)       ## only metadata

Data sets have uniform suffixes: - ref_* : the prebuilt reference expression matrix.

rnabioco/clustifyrdatahub documentation built on Nov. 11, 2023, 4:21 a.m.