View source: R/calculate_protein_abundance.R
calculate_protein_abundance | R Documentation |
Determines relative protein abundances from ion quantification. Only proteins with at least three peptides are considered for quantification. The three peptide rule applies for each sample independently.
calculate_protein_abundance( data, sample, protein_id, precursor, peptide, intensity_log2, method = "sum", for_plot = FALSE, retain_columns = NULL )
data |
a data frame that contains at least the input variables. |
sample |
a character column in the |
protein_id |
a character column in the |
precursor |
a character column in the |
peptide |
a character column in the |
intensity_log2 |
a numeric column in the |
method |
a character value specifying with which method protein quantities should be
calculated. Possible options include |
for_plot |
a logical value indicating whether the result should be only protein intensities
or protein intensities together with precursor intensities that can be used for plotting using
|
retain_columns |
a vector indicating if certain columns should be retained from the input
data frame. Default is not retaining additional columns |
If for_plot = FALSE
, protein abundances are returned, if for_plot = TRUE
also precursor intensities are returned in a data frame. The later output is ideal for plotting
with qc_protein_abundance
and can be filtered to only include protein abundances.
# Create example data data <- data.frame( sample = c( rep("S1", 6), rep("S2", 6), rep("S1", 2), rep("S2", 2) ), protein_id = c( rep("P1", 12), rep("P2", 4) ), precursor = c( rep(c("A1", "A2", "B1", "B2", "C1", "D1"), 2), rep(c("E1", "F1"), 2) ), peptide = c( rep(c("A", "A", "B", "B", "C", "D"), 2), rep(c("E", "F"), 2) ), intensity = c( rnorm(n = 6, mean = 15, sd = 2), rnorm(n = 6, mean = 21, sd = 1), rnorm(n = 2, mean = 15, sd = 1), rnorm(n = 2, mean = 15, sd = 2) ) ) data # Calculate protein abundances protein_abundance <- calculate_protein_abundance( data, sample = sample, protein_id = protein_id, precursor = precursor, peptide = peptide, intensity_log2 = intensity, method = "sum", for_plot = FALSE ) protein_abundance # Calculate protein abundances and retain precursor # abundances that can be used in a peptide profile plot complete_abundances <- calculate_protein_abundance( data, sample = sample, protein_id = protein_id, precursor = precursor, peptide = peptide, intensity_log2 = intensity, method = "sum", for_plot = TRUE ) complete_abundances
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