Description Usage Arguments Value Examples
This call will create the dataset, but the validation on the server
can take a long time. The dataset cannot be used before the
validation is complete. Use
poll_dataset_until_validated
to query the server for
the validation status. For details on what data formats are
supported by FASTGenomics refer to the documentation
here.
1 2 | create_dataset(connection, title, description, organism_id, matrix,
matrix_format, gene_nomenclature, optional_parameters = NULL)
|
connection |
The connection to be used, call
|
title |
The Title of the dataset |
description |
A description of the dataset, ca be Markdown |
organism_id |
The NCBI Taxonomy ID of your dataset, passed as an integer. Currently supported IDs are 9606 (Homo Sapiens) and 10090 (Mouse) |
matrix |
The path to your datafile in a supported format OR a dataframe. If it's a data frame it will be saved in a temporary location on your hard drive and uploaded as a file. |
matrix_format |
The format of your matrix. |
gene_nomenclature |
The gene nomenclature to be used, call
|
optional_parameters |
Further parameters to be used, eg. gene
metadata or cell metadata files. Use
|
FGResponse in case of success, FGErrorResponse if the validation failed for any reason.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | connection <- fastgenomicsRclient::connect("https://fastgenomics.org/", "Beaer ey...")
optional <- fastgenomicsRclient::FGDatasetUploadParameters(
license ="MIT",
technology = "Smart-Seq",
web_link="https://example.com",
notes="This is a TEST",
citation="FG et al",
current_normalization_status="Counts",
cell_metadata="./cell_metadata.tsv", # you can also use a dataframe directly
gene_metadata="./gene_metadata.tsv" ) # you can also use a dataframe directly
result <- fastgenomicsRclient::create_dataset(connection,
"R client test",
"description",
9606,
"./matrix.tsv" , # you can also use a dataframe directly
"sparse_cell_gene_expression",
"Entrez",
optional )
status <- fastgenomicsRclient::poll_dataset_until_validated(connection, result, 1 ) # validation messages are shown as messages
print(status) # should be TRUE
|
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