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"))