ExtractHCAMeta: Extract Metadata of Human Cell Atlas Projects with...

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

Extract Metadata of Human Cell Atlas Projects with Attributes.

Description

Extract Metadata of Human Cell Atlas Projects with Attributes.

Usage

ExtractHCAMeta(
  all.projects.df,
  organism = NULL,
  sex = NULL,
  organ = NULL,
  organ.part = NULL,
  disease = NULL,
  sample.type = NULL,
  preservation.method = NULL,
  protocol = NULL,
  suspension.type = NULL,
  cell.type = NULL,
  cell.num = NULL,
  sequencing.type = NULL
)

Arguments

all.projects.df	All detail information of HCA projects, obtained with ShowHCAProjects.
organism	The organism of the projects, choose from "Homo sapiens", "Mus musculus", "Macaca mulatta", "canis lupus familiaris", one or multiple values. Default: NULL (All).
sex	The sex of the projects, choose from "female", "male", "mixed", "unknown", one or multiple values. Default: NULL (All).
organ	The organ of the projects (e.g. brain), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).
organ.part	The organ part of the projects (e.g. cortex), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).
disease	The disease of the projects (e.g. normal), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).
sample.type	The sex of the projects, choose from "specimens", "organoids", "cellLines", one or multiple values. Default: NULL (All).
preservation.method	The preservation method of the projects (e.g. fresh), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).
protocol	The protocol of the projects (e.g. 10x 3' v2), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).
suspension.type	The suspension type of the projects, choose from "single cell", "single nucleus", "bulk cell", "bulk nuclei", one or multiple values. Default: NULL (All).
cell.type	The cell type of the projects (e.g. neuron), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).
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).
sequencing.type	The sequencing instrument type of the projects (e.g. illumina hiseq 2500), obtain available values with StatDBAttribute, one or multiple values. Default: NULL (All).

Value

Dataframe contains filtered projects.

References

https://bioconductor.org/packages/release/bioc/html/hca.html

Examples

# all available projects
all.hca.projects <- ShowHCAProjects()
# all human projects
all.human.projects <- ExtractHCAMeta(all.projects.df = all.hca.projects, organism = "Homo sapiens")
# all human and 10x 3' v2
all.human.10x.projects <- ExtractHCAMeta(
  all.projects.df = all.hca.projects,
  organism = "Homo sapiens",
  protocol = c("10x 3' v2", "10x 3' v3")
)

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