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Extract Peptide Position Start and End Columns from a QFeatures Object

extract_peptide_positions.Rd

Parses the Positions.in.Master.Proteins column from the rowData of a specified SummarizedExperiment within a QFeatures object, and extracts the start and end positions of each peptide into two new rowData columns. When multiple entries are present (semicolon-delimited), the function returns semicolon-delimited lists of start and end values.

Usage

extract_peptide_positions(qf, i, start_col = "start", end_col = "end")

Arguments

qf

A QFeatures object.

i

A single integer or character string specifying the index or name of the SummarizedExperiment within qf to operate on.

start_col

A single character string giving the name of the new column to store peptide start positions. Defaults to "start".

end_col

A single character string giving the name of the new column to store peptide end positions. Defaults to "end".

Value

The input QFeatures object with two additional columns in the rowData of the specified experiment:

start_col

Character. Semicolon-delimited start position(s) for the peptide.

end_col

Character. Semicolon-delimited end position(s) for the peptide.

Examples

if (FALSE) { # \dontrun{
library(QFeatures)
# Using default column names
qf <- extract_peptide_positions(qf, i = "peptides")

# Using custom column names
qf <- extract_peptide_positions(qf, i = 1L,
                                start_col = "pep_start",
                                end_col   = "pep_end")
} # }