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Add rowData columns with positions of PTMs with respect to peptide sequence

add_filter_ptm_pos_rowdata_mq.Rd

This function takes a SummarizedExperiment object with the evidence.txt output from MaxQuant and adds rowData columns to describe the PTMs present in the peptide and their positions within the peptide' '

Usage

add_filter_ptm_pos_rowdata_mq(
  obj,
  ptms_to_retain = c("Phospho (STY)"),
  prob_col = "Phospho..STY..Probabilities",
  min_prob = 0.501,
  filter_pep_by_prob = TRUE,
  verbose = TRUE
)

Arguments

obj

SummarizedExperiment. Proteomics dataset

ptms_to_retain

character vector with PTMs to retain. Inspect values in rowData(obj)$Modified.sequence to get correct PTM name

prob_col

character name of column containing PTM probabilities

min_prob

numeric Minimum acceptable probability for PTM localisation

filter_pep_by_prob

logical Filter the output to only return cases where the number of sites passing the probability threshold equals the number of PTMs in the peptide

verbose

logical Describe the number of PTMs detected

ptm_encoding_pos

character name vector describing whether modifification comes before (-1) or after (1) amino acid in Modified.sequence column values

Value

Returns a SummarizedExperiment with an additional column in the RowData describing the position of the PTMs with respect to the peptide sequence