import_MaxQuant: Import from MaxQuant
In arnesmits/DEP: Differential Enrichment analysis of Proteomics data

Description Usage Arguments Value Examples

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

1
2
3

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

`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.

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

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

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