scfetch (version 0.5.0)

ExtractCBDatasets: Extract UCSC Cell Browser Datasets with Attributes.

Description

Extract UCSC Cell Browser Datasets with Attributes.

Usage

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

Value

Dataframe contains filtered datasets.

Arguments

all.samples.df

Dataframe contains all samples metadata, obtained with ShowCBDatasets.

collection

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

sub.collection

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

organ

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

disease

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

organism

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

project

The project of the datasets, corresponds to projects column of ShowCBDatasets, 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(without filtering).

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)
)
}