| Title: | Cell Atlas Approximations |
| Version: | 0.1.0 |
| Maintainer: | Ying Xu <ying.xu3@unsw.edu.au> |
| Description: | Provides an interface in R to cell atlas approximations. See the vignette under "Getting started" for instructions. You can also explore the reference documentation for specific functions. Additional interfaces and resources are available at https://atlasapprox.readthedocs.io. |
| License: | MIT + file LICENSE |
| URL: | https://atlasapprox.readthedocs.io/en/latest/R/index.html, https://github.com/fabilab/cell_atlas_approximations_API |
| BugReports: | https://github.com/fabilab/cell_atlas_approximations_API/issues |
| Imports: | httr |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown |
| Config/testthat/edition: | 3 |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2024-10-23 05:53:14 UTC; yingxu |
| Author: | Fabio Zanini 
[aut],
Ying Xu [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2024-10-25 08:10:08 UTC |
GetAverage
Description
Get the average gene expression for specified features across cell types in a given organism and organ.
Usage
GetAverage(organism, organ, features)
Arguments
organism |
The organism you would like to query |
organ |
The organ you would like to query |
features |
The features (genes) you would like to query |
Value
A data.frame of average gene expression by cell type in that organism and organ
Examples
GetAverage("h_sapiens", "Lung", c("COL1A1", "PTPRC"))
GetCelltypeLocation
Description
Get the organs where a specified cell type is found in a given organism.
Usage
GetCelltypeLocation(organism, cell_type)
Arguments
organism |
The organism you would like to query |
cell_type |
The cell type you would like to query |
Value
An array of organs in which that cell type is found
Examples
GetCelltypeLocation("h_sapiens", "fibroblast")
GetCelltypes
Description
Get all available cell types for a specified organism and organ.
Usage
GetCelltypes(organism, organ)
Arguments
organism |
The organism you would like to query |
organ |
The organ you would like to query |
Value
An array of available cell types from that organism and organ
Examples
GetCelltypes("h_sapiens", "Lung")
GetDataSources
Description
Get information about the cell atlases used as data sources for the approximations.
Usage
GetDataSources()
Value
A list containing information about the cell atlases used as data sources
Examples
GetDataSources()
GetFeatures
Description
Get a list of available features (typically genes) for a specified organism.
Usage
GetFeatures(organism)
Arguments
organism |
The organism you would like to query |
Value
An array of available features (genes) from that organism
Examples
GetFeatures("h_sapiens")
GetFractionDetected
Description
Get the fraction of cells expressing specified features across cell types in a given organism and organ.
Usage
GetFractionDetected(organism, organ, features)
Arguments
organism |
The organism you would like to query |
organ |
The organ you would like to query |
features |
The features (genes) you would like to query |
Value
A data.frame of fraction of expressing cells by cell type in that organism and organ
Examples
GetFractionDetected("h_sapiens", "Lung", c("COL1A1", "PTPRC"))
GetHighestMeasurement
Description
Get the cell types with the highest expression of a specified feature in a given organism.
Usage
GetHighestMeasurement(organism, feature, number)
Arguments
organism |
The organism you would like to query |
feature |
The feature you would like to query |
number |
The number of highest expressors you would like to get |
Value
A dataframe of cell types, organs, and averages for the cell types with the highest measurement for that feature
Examples
GetHighestMeasurement("h_sapiens", "PTPRC", 5)
GetMarkers
Description
Get marker genes for a specified cell type in a given organism and organ.
Usage
GetMarkers(organism, organ, cell_type, number)
Arguments
organism |
The organism you would like to query |
organ |
The organ you would like to query |
cell_type |
The cell type you would like to query |
number |
The number of markers you would like to get |
Value
An array of markers for that cell type in that organism and organ
Examples
GetMarkers("h_sapiens", "Lung", "fibroblast", 5)
GetOrganisms
Description
Get a list of organisms available for querying in the atlasapprox api.
Usage
GetOrganisms()
Value
An array of available organisms
Examples
GetOrganisms()
GetOrgans
Description
Get all available organs for an organism
Usage
GetOrgans(organism)
Arguments
organism |
The organism you would like to query |
Value
An array of available organs from that organism
Examples
GetOrgans("h_sapiens")
GetSimilarFeatures
Description
Get features with similar expression patterns to a specified feature in a given organism and organ.
Usage
GetSimilarFeatures(organism, organ, feature, number, method)
Arguments
organism |
The organism you would like to query |
organ |
The organ you would like to query |
feature |
The feature to find similarities for |
number |
The number of similar features you would like to get. |
method |
The method used to compute similarity between features. The following methods are available: - correlation (default): Pearson correlation of the fraction_detected - cosine: Cosine similarity/distance of the fraction_detected - euclidean: Euclidean distance of average measurement (e.g. expression) - manhattan: Taxicab/Manhattan/L1 distance of average measurement - log-euclidean: Log the average measurement with a pseudocount of 0.001, then compute euclidean distance. This tends to highlight sparsely measured features |
Value
A dataframe of similar features and their distances from the focal feature according to the method chosen
Examples
GetSimilarFeatures("h_sapiens", "lung", "PTPRC", 5, "correlation")
api_version
Description
api_version
Usage
api_version
Format
An object of class character of length 1.