load_dataset: Load dataset from file
In dravishays/scandal: A framework for single-cell analysis

Description Usage Arguments Value Author(s)

Loads a dataset from file

load_dataset(
  filename,
  type = "tsv",
  cell_2_node_map = DEFAULT_CELL_2_NODE_MAP,
  drop_cols = 1L,
  rownames_col = 1L,
  excluded_samples = NULL,
  as_Matrix = TRUE,
  umi_to_upm = TRUE,
  verbose = FALSE
)

`filename`	the name of the file containing the dataset (in tab-delimited format). In case of 10x data expects a path to a folder containing the 3 output files of cellranger (barcodes, features and matrix).
`type`	either tsv (tab-delimited text file), rds (binary R data file) or 10x (umi counts data). Default is tsv.
`cell_2_node_map`	a function that maps a vector of cell IDs to a vector of node IDs to which the cells belong. The default function assumes that the cell ID is a string separated by "-" and that the node ID is contained in the substring until the first "-" character.
`drop_cols`	number of columns that should be dropped from the dataset, i.e. if drop_cols == 3 then columns 1:3 will be dropped. Default is 1.
`rownames_col`	the column that contains the rownames, i.e. gene symbols or identifiers. Default is 1.
`excluded_samples`	a vector containing the names of the samples that should be excluded from the returned dataset. Defaults to NULL.
`as_Matrix`	logical indicating whether the loaded dataset should be returned as an S4 Matrix class (supports sparse representation) or base R matrix type. Default is TRUE.
`umi_to_upm`	Convert UMI counts to UMI per million units (e.g. CPM). Valid only for 10x data. Default is TRUE.
`verbose`	suppresses all messages from this function. Default is FALSE.