import_MaxQuant {DEP} | R Documentation

## Import from MaxQuant

### Description

`import_MaxQuant` imports a protein table from MaxQuant and converts it into a SummarizedExperiment object.

### Usage

    import_MaxQuant(proteins, expdesign, filter = c("Reverse",
      "Potential.contaminant"), intensities = "LFQ", names = "Gene.names",
      ids = "Protein.IDs", delim = ";")

### Arguments

`proteins` | Data.frame, Protein table originating from MaxQuant.
`expdesign` | Data.frame, Experimental design with 'label', 'condition' and 'replicate' information. See `UbiLength_ExpDesign` for an example experimental design.
`filter` | Character, Name of the column(s) containing features to be filtered on.
`intensities` | Character(1), Prefix of the columns containing sample intensities.
`names` | Character(1), Name of the column containing feature names.
`ids` | Character(1), Name of the column containing feature IDs.
`delim` | Character(1), Sets the delimiter separating the feature names within on protein group.

### Value

A SummarizedExperiment object with log2-transformed values and "name" and "ID" columns containing unique names and identifiers.

### Examples

    # Load example data and experimental design
    data <- UbiLength
    exp_design <- UbiLength_ExpDesign

    # Import data
    se <- import_MaxQuant(data, exp_design)

[Package DEP version 1.9.0 Index]