make_TMT_se: Data.frame to SummarizedExperiment object conversion using...

Description Usage Arguments Value Examples

Description

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

Usage

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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

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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 = "_")
}

demar01/protrusionproteome documentation built on April 29, 2021, 5:47 a.m.