Extract Cell Type Composition of UCSC Cell Browser Datasets.

Extract Cell Type Composition of UCSC Cell Browser Datasets.

Usage

ExtractCBComposition(
  json.folder = NULL,
  sample.df = NULL,
  all.samples.df = NULL,
  collection = NULL,
  sub.collection = NULL,
  organ = NULL,
  disease = NULL,
  organism = NULL,
  project = NULL,
  fuzzy.match = TRUE,
  cell.num = NULL
)

Arguments

json.folder

Folder contains datasets json files, same as json.folder of ShowCBDatasets. Default: NULL (current working directory).

sample.df

Dataframe contains used datasets. Default: NULL.

all.samples.df

Dataframe contains all samples metadata, obtained with ShowCBDatasets. Default: NULL. sample.df and all.samples.df cannot be both NULL.

collection

The collection of the datasets, corresponds to shortLabel column of all.samples.df, obtain available values with StatDBAttribute. Default: NULL (without filtering).

sub.collection

The sub-collection of the datasets, corresponds to subLabel column of all.samples.df, obtain available values with StatDBAttribute. Default: NULL (without filtering).

organ

The organ of the datasets, corresponds to body_parts column of all.samples.df, obtain available values with StatDBAttribute. Default: NULL (without filtering).

disease

The disease of the datasets, corresponds to diseases column of all.samples.df, obtain available values with StatDBAttribute. Default: NULL (without filtering).

organism

The specie of the datasets, corresponds to organisms column of all.samples.df, obtain available values with StatDBAttribute. Default: NULL (without filtering).

project

The project of the datasets, corresponds to projects column of all.samples.df, obtain available values with StatDBAttribute. Default: NULL (without filtering).

fuzzy.match

Logical value, whether to perform fuzzy match with provided attribute values. Default: TRUE.

cell.num

Cell number filter. If NULL, no filter; if one value, lower filter; if two values, low and high filter. Deault: NULL.

Value

Dataframe contains sample information and cell type composition.

Examples

if (FALSE) {
# lazy mode, load datasets json files locally, need users to provide json folder
ucsc.cb.samples <- ShowCBDatasets(lazy = TRUE, json.folder = NULL, update = FALSE)
# cell number is between 1000 and 2000
hbb.sample.df <- ExtractCBDatasets(
  all.samples.df = ucsc.cb.samples, organ = c("brain", "blood"),
  organism = "Human (H. sapiens)", cell.num = c(1000, 2000)
)
hbb.sample.ct <- ExtractCBComposition(json.folder = NULL, sample.df = hbb.sample.df)
}