import_IsobarQuant {DEP} | R Documentation |
import_IsobarQuant
imports a protein table from IsobarQuant
and converts it into a SummarizedExperiment object.
import_IsobarQuant(proteins, expdesign, intensities = "signal_sum", names = "gene_name", ids = "protein_id", delim = "[|]")
proteins |
Data.frame, Protein table for which unique names will be created. |
expdesign |
Data.frame,
Experimental design with 'label', 'condition'
and 'replicate' information.
See |
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.
## Not run: # Load data isobarquant_table <- read.csv("testfile.txt", header = TRUE, stringsAsFactors = FALSE, sep = "\t") exp_design <- read.csv("test_experimental_design.txt", header = TRUE, stringsAsFactors = FALSE, sep = "\t") # Import data se <- import_IsobarQuant(isabarquant_table, exp_design) ## End(Not run)