ExtractCBComposition: Extract Cell Type Composition of UCSC Cell Browser Datasets.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Extract Cell Type Composition of UCSC Cell Browser Datasets.

Description

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

## Not run: 
# 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)

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.