import_MaxQuant {DEP} | R Documentation |
import_MaxQuant
imports a protein table from MaxQuant
and converts it into a SummarizedExperiment object.
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 |
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)