This function takes a Qfeatures object with the evidence.txt
output from MaxQuant and filters it to retain peptides with a given PTM.
Usage
filter_maxquant_ptm(obj, i, ptm_prob_col = "Phospho..STY..Probabilities")
Arguments
- obj
QFeatures. Proteomics dataset
- i
string. Index for the SummarizedExperiment with data without imputation
- ptm_prob_col
character column name for PTMs.
Value
Returns a SummarizedExperiment where the value for the PTM probability column is not empty