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

add_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_ptm_pos_rowdata_mq(
  obj,
  ptms_to_retain = c("p", "(ph)", "(ac)p"),
  ptm_encoding_pos = c(p = -1, `(ph)` = 1, `(ac)p` = -1, `(ox)` = 1),
  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

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