make_TMT_se: Data.frame to SummarizedExperiment object conversion using...
In demar01/protrusionproteome: protrusionproteome

Description Usage Arguments Value Examples

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 = "_"
)

`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

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

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 = "_")
}