metamorphr (version 0.2.0)

filter_msn: Filter Features based on occurrence of fragment ions

Description

Filters Features based on the presence of MSn fragments. This can help, for example with the identification of potential homologous molecules.

Usage

filter_msn(
  data,
  fragments,
  min_found,
  tolerance = 5,
  tolerance_type = "ppm",
  show_progress = TRUE
)

Value

A filtered tibble.

Arguments

data

A data frame containing MSn spectra.

fragments

A numeric. Exact mass of the fragment(s) to filter by.

min_found

How many of the fragments must be found in order to keep the row? If min_found = length(fragments), all fragments must be found.

tolerance

A numeric. The tolerance to apply to the fragments. Either an absolute value in Da (if tolerance_type = "absolute") or in ppm (if tolerance_type = "ppm").

tolerance_type

Either "absolute" or "ppm". Should the tolerance be an absolute value or in ppm?

show_progress

A logical indicating whether the progress of the filtering should be printed to the console. Only important for large tibbles.

Examples

# all of the given fragments (3) must be found
# returns the first row of toy_mgf
toy_mgf %>%
  filter_msn(fragments = c(12.3456, 23.4567, 34.5678), min_found = 3)

# all of the given fragments (3) must be found
# returns an empty tibble because the third fragment
# of row 1 (34.5678)
# is outside of the tolerance (5 ppm):
# Lower bound:
# 34.5688 - 34.5688 * 5 / 1000000 = 34.5686
# Upper bound:
# 34.5688 + 34.5688 * 5 / 1000000 = 34.5690
toy_mgf %>%
  filter_msn(fragments = c(12.3456, 23.4567, 34.5688), min_found = 3)

# only 2 of the 3 fragments must be found
# returns the first row of toy_mgf
toy_mgf %>%
  filter_msn(fragments = c(12.3456, 23.4567, 34.5688), min_found = 2)