create_dataset_df: Submits a data set from a sparse matrix of dgTmatrix type and...

In FASTGenomics/r_client: Manage FASTGenomics Instances

Description

dgTMatrix has to have named dimensions, cell and gene metadata must have cellId and geneId columns respectively. The names of the dimensions in the matrix must be a subset of the respective gene/cell metadata data frames.

Usage

create_dataset_df(connection, matrix, cell_metadata, gene_metadata,
  gene_nomenclature, organism_id, title, zipfiles = TRUE,
  description = "", optional_parameters = FGDatasetUploadParameters(),
  tmpdir = NULL)

Arguments

connection	FASTGenomics connection object
matrix	sparseMatrix storing the expression table. The first dimension is assumed to be genes and the second must be cell names.
cell_metadata	dataframe with cell metadata, must have a cellId column.
gene_metadata	dataframe with gene metadata, must have a geneId column.
organism_id	One of 9606 (Mouse) and 10090 (Human)
title	The title of the data set
zipfiles	Weather to compress files before submitting, Default: TRUE
description	long description, Default: ""
optional_parameters	Object representing further optional parameters, see FGDatasetUploadParameters, Default: NULL The properties batch_column, gene_metadata and cell_metadata of this object are always ignored
tmpdir	The location of temporary files, Default: NULL

Value

either of FGResponse, FGErrorResponse, FGErrorModelResponse, FGValidationProblem.

FASTGenomics/r_client documentation built on June 25, 2019, 12:12 a.m.