Merges the analytical replicates of an experiment

Usage

replicate_sum(
  data,
  metadata_sample = NULL,
  metadata_info = c(Conditions = "Conditions", Biological_Replicates =
    "Biological_Replicates", Analytical_Replicates = "Analytical_Replicates"),
  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 which contains 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 information about the samples, which will be combined with the input data based on the unique sample identifiers used as rownames. Must contain column with Conditions. If you do not have multiple conditions in your experiment assign all samples into the same condition. Default = NULL
metadata_info: Optional: Named vector including the Conditions and Replicates information: c(Conditions="ColumnNameConditions", Biological_Replicates="ColumnName_metadata_sample", Analytical_Replicates="ColumnName_metadata_sample").Default = NULL
save_table: Optional: File types for the analysis results are: "csv", "xlsx", "txt", ot NULL default: "csv"
path: Optional: Path to the folder the results should be saved at. default: NULL

Value

DF with the merged analytical replicates

Examples

data(intracell_raw_se)
Res <- replicate_sum(data = intracell_raw_se)

data(intracell_raw)
Intra <- intracell_raw %>% tibble::column_to_rownames("Code")
Res <- replicate_sum(
    data = Intra[-c(49:58), -c(1:3)],
    metadata_sample = Intra[-c(49:58), c(1:3)]
)