This function takes a data frame of proteomics data and its corresponding sample metadata to construct a SummarizedExperiment object. It handles detection of intensity columns, validation, and synchronization of metadata.

Usage

create_se(
  data,
  sample_metadata = NULL,
  intensity_cols = NULL,
  creation_method = "Unknown"
)

Arguments

data: A data frame containing both protein metadata and intensity values.
sample_metadata: A data frame for sample metadata. It must contain a 'SampleID' column that matches the intensity column headers in 'data'. If NULL (the default), a basic metadata table is generated from the column names.
intensity_cols: An optional character or numeric vector specifying which columns in 'data' are the intensity/abundance columns. If NULL, the function will attempt to autodetect them as all numeric columns.
creation_method: A character string to log how the data was created (e.g., "MaxQuant_LFQ"). Stored in the object's metadata.

Value

A SummarizedExperiment object.

Examples

# --- Sample Data ---
test_data <- data.frame(
  ProteinID = c("P02768", "P01023", "P10636"),
  Gene = c("ALB", "A2M", "CALM1"),
  Sample_A_1 = c(10.1, 12.5, 13.2),
  Sample_A_2 = c(10.5, 12.8, 13.9),
  Sample_B_1 = c(15.2, 18.1, 19.0),
  Sample_B_2 = c(15.8, 18.5, 19.9)
)

sample_info <- data.frame(
  SampleID = c("Sample_A_1", "Sample_A_2", "Sample_B_1", "Sample_B_2"),
  Condition = c("A", "A", "B", "B")
)

# --- Function Call ---
se <- create_se(
  data = test_data,
  sample_metadata = sample_info
)
#> `intensity_cols` not provided. Detecting numeric columns as intensity data.

# --- Inspect the new object ---
print(se)
#> class: SummarizedExperiment 
#> dim: 3 4 
#> metadata(2): creation_method processing_log
#> assays(1): intensities
#> rownames: NULL
#> rowData names(2): ProteinID Gene
#> colnames(4): Sample_A_1 Sample_A_2 Sample_B_1 Sample_B_2
#> colData names(1): Condition
SummarizedExperiment::assayNames(se)
#> [1] "intensities"
head(SummarizedExperiment::rowData(se))
#> DataFrame with 3 rows and 2 columns
#>     ProteinID        Gene
#>   <character> <character>
#> 1      P02768         ALB
#> 2      P01023         A2M
#> 3      P10636       CALM1
SummarizedExperiment::colData(se)
#> DataFrame with 4 rows and 1 column
#>              Condition
#>            <character>
#> Sample_A_1           A
#> Sample_A_2           A
#> Sample_B_1           B
#> Sample_B_2           B
S4Vectors::metadata(se)
#> $creation_method
#> [1] "Unknown"
#> 
#> $processing_log
#> list()
#>