Download UCSC Cell Browser Datasets.

Download UCSC Cell Browser Datasets.

Usage

ParseCBDatasets(
  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,
  timeout = 1000,
  obs.value.filter = NULL,
  obs.keys = NULL,
  include.genes = NULL,
  merge = TRUE
)

Arguments

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.

timeout

Maximum request time when loading data online. Default: 1000.

obs.value.filter

Filter expression for cell's metadata, e.g., `Louvain Cluster` == 1 & sex == 'M' (use `` to wrap columns with space). Default: NULL.

obs.keys

Columns to fetch for the cell's metadata. e.g., c("cluster", "Louvain Cluster", "donor","sex"). Default: NULL.

include.genes

Genes to include. Default: NULL.

merge

Logical value, whether to merge Seurat list. Default: FALSE.

Value

Seurat object (if merge is TRUE) or list of Seurat objects (if merge is FALSE).

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.seu <- ParseCBDatasets(sample.df = hbb.sample.df)
# test 10x and matrix load
complex.df <- ucsc.cb.samples[c(1, 927, 379), ] # two 10x and one matrix
complex.seu.list <- ParseCBDatasets(sample.df = test.df, merge = F)
}