Extract Metadata of Human Cell Atlas Projects with Attributes.

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

# \donttest{
# all available projects
all.hca.projects <- ShowHCAProjects()
# all human projects
all.human.projects <- ExtractHCAMeta(all.projects.df = all.hca.projects, organism = "Homo sapiens")
#> Use all biologicalSex as input!
#> Use all organ as input!
#> Use all organPart as input!
#> Use all disease as input!
#> Use all sampleEntityType as input!
#> Use all preservationMethod as input!
#> Use all libraryConstructionApproach as input!
#> Use all nucleicAcidSource as input!
#> Use all selectedCellType as input!
#> Use all instrumentManufacturerModel as input!
# 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")
)
#> Use all biologicalSex as input!
#> Use all organ as input!
#> Use all organPart as input!
#> Use all disease as input!
#> Use all sampleEntityType as input!
#> Use all preservationMethod as input!
#> Use all nucleicAcidSource as input!
#> Use all selectedCellType as input!
#> Use all instrumentManufacturerModel as input!
# }