trace_all_levels {flowTraceR}

Trace common and unique identifications between different software outputs for all levels

Description

Identifications of two input data frames are compared and categorized in unique and common entries for each level.

Usage

trace_all_levels(
  input_df1,
  input_df2,
  analysis_name1 = "input_df1",
  analysis_name2 = "input_df2",
  filter_unknown_mods = TRUE
)

Arguments

input_df1

A tibble with flowTraceR's standardized precursor, modified peptide and proteinGroup level information.

input_df2

A tibble with flowTraceR's standardized precursor, modified peptide and proteinGroup level information.

analysis_name1

output tibble name for input_df1 - default is "input_df1".

analysis_name2

output tibble name for input_df2 - default is "input_df2".

filter_unknown_mods

Logical value, default is TRUE. If TRUE, unknown modifications are filtered out - requires "traceR_precursor_unknownMods" or "traceR_mod.peptides_unknownMods" column.

Details

Based on flowTraceR's standardized output format two software outputs can be compared and categorized into common and unique identifications - for precursor, modified peptide and proteinGroup level.

Value

This function returns a list with both original submitted tibbles - input_df1 and input_df2 - with the following new columns:

• traceR_traced_precursor - categorization on precursor level in common and unique entries.

• traceR_traced_mod.peptides - categorization on modified peptide level in common and unique entries.

• traceR_traced_proteinGroups - categorization on proteinGroups level in common and unique entries.

Author(s)

Oliver Kardell

Examples

# Load libraries
library(dplyr)
library(stringr)
library(tibble)

# DIA-NN example data
diann <- tibble::tibble(
  "traceR_proteinGroups" = c("P02768", "P02671", "Q92496", "DummyProt"),
  "traceR_mod.peptides" = c("AAC(UniMod:4)LLPK", "RLEVDIDIK",
   "EGIVEYPR", "ALTDM(DummyModification)PQMK"),
  "traceR_mod.peptides_unknownMods" = c(FALSE, FALSE, FALSE, TRUE),
  "traceR_precursor" = c("AAC(UniMod:4)LLPK1", "RLEVDIDIK2",
   "EGIVEYPR2", "ALTDM(DummyModification)PQMK3" ),
  "traceR_precursor_unknownMods" = c(FALSE, FALSE, FALSE, TRUE)
)
# Spectronaut example data
spectronaut <- tibble::tibble(
  "traceR_proteinGroups" = c("P02768", "Q02985", "P02671"),
  "traceR_mod.peptides" = c("AAC(UniMod:4)LLPK", "EGIVEYPR", "M(UniMod:35)KPVPDLVPGNFK"),
  "traceR_mod.peptides_unknownMods" = c(FALSE, FALSE, FALSE),
  "traceR_precursor" = c("AAC(UniMod:4)LLPK1", "EGIVEYPR2", "M(UniMod:35)KPVPDLVPGNFK2"),
  "traceR_precursor_unknownMods" = c(FALSE, FALSE, FALSE)
)

# trace all levels in one step
traced_all <- trace_all_levels(
  input_df1 = diann,
  input_df2 = spectronaut,
  analysis_name1 = "DIA-NN",
  analysis_name2 = "Spectronaut",
  filter_unknown_mods = TRUE
)