Read and standardize sample metadata for VISTA

read_vista_metadata() standardizes a sample sheet for use as sample_info in create_vista(). It infers or creates the required sample_names column using the same conventions VISTA already accepts in the constructor.

Usage

read_vista_metadata(
  x,
  sample_column = NULL,
  required_columns = NULL,
  drop_empty = TRUE,
  standardize_names = TRUE,
  verbose = TRUE
)

Arguments

x

Sample metadata as a data frame or file path.

sample_column

Optional column to use as sample_names. If omitted, VISTA uses an existing sample_names column, non-default rownames, or common aliases such as sample, sample_id, or Run.

required_columns

Optional character vector of columns that must be present after import.

drop_empty

Logical; if TRUE, remove columns that are entirely NA or empty strings.

standardize_names

Logical; if TRUE, coerce the final sample_names column to character and set rownames to match it.

verbose

Logical; print an informational import summary.

Value

A data frame suitable for use as sample_info in create_vista().

Examples

data("sample_metadata", package = "VISTA")

si <- read_vista_metadata(sample_metadata[seq_len(6), ])
#> Imported 6 samples with 13 metadata columns.
head(si$sample_names)
#> [1] "SRR1039508" "SRR1039509" "SRR1039512" "SRR1039513" "SRR1039516"
#> [6] "SRR1039517"