diann_maxlfq | R Documentation |
Quantify using the MaxLFQ algorithm https://doi.org/10.1074/mcp.M113.031591. This function can be used to calculate protein quantities from peptide/precursor/fragment quantities or, for example, to calculate peptide quantities from precursor/fragment quantities. Totally based on function from diann-rpackage from Vadim Demichev
diann_maxlfq(
x,
sample.header = "File.Name",
group.header = "Protein.Names",
id.header = "Precursor.Id",
quantity.header = "Precursor.Normalised",
margin = -10,
count_pep = TRUE,
only_countsall = FALSE,
Top3 = FALSE
)
x |
data, output from diann_load |
sample.header |
Sample id column name |
group.header |
Colulmn name corresponding to the group Id, e.g. protein Id |
id.header |
Id column name (protein, gene, ...) |
quantity.header |
Quantity column name |
margin |
quantities below exp(margin) might be treated as NA |
count_pep |
logical; get peptide count? |
only_countsall |
logical; should only keep peptide counts all or also peptide counts for each fractions? |
Top3 |
logical; get Top3 absolute quantification |
A dataframe containing the quantities from the id you selected
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