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Ying Xu [aut, cre]| Title: | Cell Atlas Approximations |
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| 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>. |
| Authors: | Fabio Zanini [aut] ,
Ying Xu [aut, cre] |
| Maintainer: | Ying Xu <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2024-10-26 03:32:58 UTC |
| Source: | CRAN |
api_version
api_versionapi_version
An object of class character of length 1.
Get the average gene expression for specified features across cell types in a given organism and organ.
GetAverage(organism, organ, features)GetAverage(organism, organ, features)
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 |
A data.frame of average gene expression by cell type in that organism and organ
GetAverage("h_sapiens", "Lung", c("COL1A1", "PTPRC"))GetAverage("h_sapiens", "Lung", c("COL1A1", "PTPRC"))
Get the organs where a specified cell type is found in a given organism.
GetCelltypeLocation(organism, cell_type)GetCelltypeLocation(organism, cell_type)
organism |
The organism you would like to query |
cell_type |
The cell type you would like to query |
An array of organs in which that cell type is found
GetCelltypeLocation("h_sapiens", "fibroblast")GetCelltypeLocation("h_sapiens", "fibroblast")
Get all available cell types for a specified organism and organ.
GetCelltypes(organism, organ)GetCelltypes(organism, organ)
organism |
The organism you would like to query |
organ |
The organ you would like to query |
An array of available cell types from that organism and organ
GetCelltypes("h_sapiens", "Lung")GetCelltypes("h_sapiens", "Lung")
Get information about the cell atlases used as data sources for the approximations.
GetDataSources()GetDataSources()
A list containing information about the cell atlases used as data sources
GetDataSources()GetDataSources()
Get a list of available features (typically genes) for a specified organism.
GetFeatures(organism)GetFeatures(organism)
organism |
The organism you would like to query |
An array of available features (genes) from that organism
GetFeatures("h_sapiens")GetFeatures("h_sapiens")
Get the fraction of cells expressing specified features across cell types in a given organism and organ.
GetFractionDetected(organism, organ, features)GetFractionDetected(organism, organ, features)
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 |
A data.frame of fraction of expressing cells by cell type in that organism and organ
GetFractionDetected("h_sapiens", "Lung", c("COL1A1", "PTPRC"))GetFractionDetected("h_sapiens", "Lung", c("COL1A1", "PTPRC"))
Get the cell types with the highest expression of a specified feature in a given organism.
GetHighestMeasurement(organism, feature, number)GetHighestMeasurement(organism, feature, number)
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 |
A dataframe of cell types, organs, and averages for the cell types with the highest measurement for that feature
GetHighestMeasurement("h_sapiens", "PTPRC", 5)GetHighestMeasurement("h_sapiens", "PTPRC", 5)
Get marker genes for a specified cell type in a given organism and organ.
GetMarkers(organism, organ, cell_type, number)GetMarkers(organism, organ, cell_type, number)
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 |
An array of markers for that cell type in that organism and organ
GetMarkers("h_sapiens", "Lung", "fibroblast", 5)GetMarkers("h_sapiens", "Lung", "fibroblast", 5)
Get a list of organisms available for querying in the atlasapprox api.
GetOrganisms()GetOrganisms()
An array of available organisms
GetOrganisms()GetOrganisms()
Get all available organs for an organism
GetOrgans(organism)GetOrgans(organism)
organism |
The organism you would like to query |
An array of available organs from that organism
GetOrgans("h_sapiens")GetOrgans("h_sapiens")
Get features with similar expression patterns to a specified feature in a given organism and organ.
GetSimilarFeatures(organism, organ, feature, number, method)GetSimilarFeatures(organism, organ, feature, number, method)
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 |
A dataframe of similar features and their distances from the focal feature according to the method chosen
GetSimilarFeatures("h_sapiens", "lung", "PTPRC", 5, "correlation")GetSimilarFeatures("h_sapiens", "lung", "PTPRC", 5, "correlation")