formatForAnalysis {ASICS} | R Documentation

## Format data for analysis

### Description

Create an object of class `SummarizedExperiment` to use in functions `pca`, `oplsda` or `kruskalWallis`.

### Usage

    formatForAnalysis(
      data,
      design = NULL,
      feature_info = NULL,
      zero.threshold = 100,
      zero.group = NULL,
      outliers = NULL
    )

### Arguments

`data` | A data frame containing omics dataset with samples in columns and features of interest in rows (metabolites/buckets...).
`design` | A data frame describing the colums of `data` with at least two columns, the first one corresponding to the column names of `data`. Default to NULL (in which case, the column names of `data` are used for study design).
`feature_info` | A data frame describing the rows of `data` with at least two columns, the first one corresponding to the row names of `data`. Default to NULL (in which case, the row names of `data` are used for feature information).
`zero.threshold` | Remove features having a proportion of zeros larger than or equal to `zero.threshold`. Default to `100`.
`zero.group` | Variable name of design data frame specifying the group variable used to remove features with a proportion of zeros larger than or equal to `zero.threshold` within the group. Default to `NULL`, no group.
`outliers` | Names of the outliers (samples) to remove.

### Value

An object of type `SummarizedExperiment` with metabolite data given as buckets or quantified metabolites.

### Examples

    # Import quantification results
    if (require("ASICSdata", quietly = TRUE)) {
      quantif_path <- system.file("extdata", "results_ASICS.txt",
                                  package = "ASICSdata")
      quantification <- read.table(quantif_path, header = TRUE, row.names = 1)

      # Import design
      design <- read.table(system.file("extdata", "design_diabete_example.txt",
                                       package = "ASICSdata"), header = TRUE)

      # Create object for analysis and remove features with more than 25% of
      # zeros
      analysis_obj <- formatForAnalysis(quantification,
                                        design = design,
                                        zero.threshold = 25,
                                        zero.group = "condition")
    }

[Package ASICS version 2.3.1 Index]