Meta prior-knowledge

Usage

meta_pk(
  data,
  metadata_sample,
  metadata_info = NULL,
  save_table = "csv",
  path = NULL
)

Arguments

data: SummarizedExperiment (se) file including assay and colData. If se file is provided, metadata_sample is extracted from the colData of the se object. Alternatively provide a DF with unique sample identifiers as row names and metabolite numerical values in columns with metabolite identifiers as column names. Use NA for metabolites that were not detected.
metadata_sample: Optional: Only required if you did not provide se file in parameter data. Provide DF which contains metadata information about the samples, which will be combined with your input data based on the unique sample identifiers used as rownames. Default = NULL
metadata_info: Optional: NULL or vector with column names that should be used, i.e. c("Age", "gender", "Tumour-stage"). default: NULL
save_table: Optional: File types for the analysis results are: "csv", "xlsx", "txt". Default = "csv"
path: Optional: Path to the folder the results should be saved at. default: NULL

Value

DF with prior knowledge based on patient metadata

Examples

data(tissue_norm_se)
Res <- meta_pk(tissue_norm_se)

data(tissue_norm)
Tissue_Norm <- tissue_norm %>% tibble::column_to_rownames("Code")
Res <- meta_pk(
    data = Tissue_Norm[, -c(1:13)],
    metadata_sample = Tissue_Norm[, c(2, 4:5, 12:13)]
)