Data.frame to SummarizedExperiment object conversion using file information and user input

make_TMT_se creates a SummarizedExperiment object based on protein table and user's input about experimental design.

make_TMT_se(
  proteins_unique,
  columns_positions,
  intensities,
  time_unit = 30,
  time_span = c(1, 2, 4, 8, 16),
  numerator = "prot",
  denominator = "body",
  sep = "_"
)

Arguments

proteins_unique	Data.frame, Protein table with unique names annotated in the 'name' column (output from make_unique()).
columns_positions	Integer, position of columns that contain experiment quantitative data
intensities	Character, names of columns that contain experiment quantitative data
time_unit	Integer, unit of time in that defines the experiment
time_span	Integer, number of times that the time_unit is repeated at the experimental timepoint
numerator	Character, condition of interest (prot)
denominator	character, condition to make relative (body)
sep	Character, The separator used to parse the column header

Value

A SummarizedExperiment object with log2-transformed values, normalised to control and median subtracted (by column).

Examples

if(interactive()){
# Load example
data <- prot.raw
data <- data[data$Reverse != "+" & data$Potential.contaminant != "+" &
data$Reverse != "+" ,]
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")

columns_positions<-str_which(colnames(data_unique),
"Reporter.intensity.corrected.(\\d)+.(\\d)")
intensities <- colnames(data_unique)[str_which(colnames(data_unique),
"Reporter.intensity.corrected.(\\d)+.(\\d)")]
# Make SummarizedExperiment
se <- make_TMT_se(data_unique,columns_positions,intensities,
time_unit=30,
time_span=c(1,2,4,8,16),
numerator= "prot",
denominator= "body",
sep = "_")
}