Package 'scaeData'

Split getter output

Description

Internal function used by ehoub_out() that splits the output from the getter into a file path and the corresponding file name. This is necessary as the read-in function read_allele_counts() from the SingleCellAlleleExperiment package expects a directory path as well as the names of each expected file.

Usage

demo_dir_file(ehub_dir, dir = TRUE)

Arguments

ehub_dir	character string that is retrieved by the getters
dir	binary if the output should contain file path and file name or only file name

Value

list containing (file path) and file name

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Build output list per dataset

Description

Internal function used by scaeDataGet() to build a list containing the file path

Usage

ehub_out(bc_dir, feature_dir, mtx_dir)

Arguments

bc_dir	character string containing full path to barcode file
feature_dir	character string containing full path to feature file
mtx_dir	character string containing full path to matrix file

Value

list with four elements containing file path to the directory containing all files and each file name for barcodes, features and matrix

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Get barcode identifiers for ⁠pbmc-10k⁠ dataset

Description

Internal getter function that retrieves the pbmc_10k_barcodes.txt from ExperimentHub (eh[["EH9456"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_barcodes_10k()

Value

character string containing the file path of the barcode file

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Get barcode identifiers for ⁠pbmc-20k⁠ dataset

Description

Internal getter function that retrieves the pbmc_20k_barcodes.txt from ExperimentHub (eh[["EH9459"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_barcodes_20k()

Value

character string containing the file path of the barcode file

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Get barcode identifiers for ⁠pbmc-5k⁠ dataset

Description

Internal getter function that retrieves the pbmc_5k_barcodes.txt from ExperimentHub (eh[["EH9453"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_barcodes_5k()

Value

character string containing the file path of the barcode file

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Get quantification matrix for ⁠pbmc-10k⁠ dataset

Description

Internal getter function that retrieves the pbmc_10k_count_mtx.mtx from ExperimentHub (eh[["EH9458"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_counts_10k()

Value

character string containing the file path of the matrix file

---

Get quantification matrix for ⁠pbmc-20k⁠ dataset

Description

Internal getter function that retrieves the pbmc_20k_count_mtx.mtx from ExperimentHub (eh[["EH9461"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_counts_20k()

Value

character string containing the file path of the matrix file

---

Get quantification matrix for ⁠pbmc-5k⁠ dataset

Description

Internal getter function that retrieves the pbmc_5k_count_mtx.mtx from ExperimentHub (eh[["EH9455"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_counts_5k()

Value

character string containing the file path of the matrix file

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Get feature identifiers for ⁠pbmc-10k⁠ dataset

Description

Internal getter function that retrieves the pbmc_10k_features.txt from ExperimentHub (eh[["EH9457"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_features_10k()

Value

character string containing the file path of the feature file

---

Get feature identifiers for ⁠pbmc-20k⁠ dataset

Description

Internal getter unction that retrieves the pbmc_20k_features.txt from ExperimentHub (eh[["EH9460"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_features_20k()

Value

character string containing the file path of the feature file

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Get feature identifiers for ⁠pbmc-5k⁠ dataset

Description

Internal getter function that retrieves the pbmc_5k_features.txt from ExperimentHub (eh[["EH9454"]]). This is one out of 3 files that are necessary to load for using the data in a SingleCellAlleleExperiment data structure. File is generated with the scIGD workflow.

Usage

get_features_5k()

Value

character string containing the file path of the features file

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Download and process demo dataset

Description

Wrapper function used to retrieve a list containing the file path and file names for the chosen dataset. The corresponding dataset is retrieved from ExperimentHub. The following demo datasets are available:

• pbmc_5k: using the following ExperimentHub entries: barcodes(EH9453); features(EH9454); counts matrix(EH9455)

• pbmc_10k: using the following ExperimentHub entries: barcodes(EH9456); features(EH9457); counts matrix(EH9458)

• pbmc_20k: using the following ExperimentHub entries: barcodes(EH9459); features(EH9460); counts matrix(EH9461)

Usage

scaeDataGet(dataset = c("pbmc_5k", "pbmc_10k", "pbmc_20k"))

Arguments

dataset

character vector describing which dataset should be retrieved. Choose one as input.

Value

list with four elements containing file path and file names for the chosen dataset

Examples

if (interactive()) {
    scae_data_5k <- scaeDataGet(dataset = "pbmc_5k")
    scae_data_5k
}

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