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Edit or customize a platform ingestion configuration table

Source: R/ingest_config.R
ingest_config.Rd

Facilitates viewing, adding, adjusting, or auto-configuring regex patterns and annotation mappings in a platform configuration TSV file. Works seamlessly with export_config() and input_audit().

Usage

ingest_config(
  platform = NULL,
  analyte = c("proteins", "peptides"),
  config_file = NULL,
  action = c("view", "set", "add", "remove", "auto_fix"),
  category = NULL,
  column_defined = NULL,
  column_import = NULL,
  pattern_extract = NULL,
  pattern_remove = NULL,
  pattern_split = NULL,
  pivot = NULL,
  file_name = NULL,
  use_lfq = NULL,
  save = TRUE,
  output_file = NULL
)

Arguments

platform

Platform source (e.g. 'MaxQuant', 'ProteomeDiscoverer', 'FragPipe', 'DIA-NN')

analyte

Omics analyte ('proteins', 'peptides')

config_file

Optional path to a specific config TSV file. If NULL, targets <platform>_<analyte>.tsv in current directory.

action

Action to execute: 'view', 'set', 'add', 'remove', 'auto_fix'

category

Category for the entry ('identifier', 'quantitative', 'accounting', 'annotation', 'sample', 'impute')

column_defined

Variable name in tidyproteomics (e.g. 'gene_name', 'description', 'abundance_raw', 'protein')

column_import

Regex pattern to match the raw file column header (e.g. '^Gene names$', '^LFQ intensity\s')

pattern_extract

Optional regex pattern to extract substring

pattern_remove

Optional regex pattern to remove

pattern_split

Optional regex pattern to split (e.g. '\;')

pivot

Optional boolean (TRUE for quantitative/accounting sample-pivoted columns)

file_name

Optional raw data file path required when action = 'auto_fix'

use_lfq

Optional logical when action = 'auto_fix', whether to prioritize MaxLFQ intensity (default: TRUE if LFQ present)

save

Logical, whether to write the updated configuration to disk (default: TRUE)

output_file

Output TSV path. Defaults to config_file or <platform>_<analyte>.tsv.

Value

A tibble of the modified configuration table (invisibly)

Examples

library(tidyproteomics)
if (FALSE) {
# View current config
ingest_config("MaxQuant", "proteins", action = "view")

# Add an annotation
ingest_config("MaxQuant", "proteins", action = "add",
              category = "annotation", column_defined = "gene_name",
              column_import = "^Gene names$")

# Update quantitative layer to MaxLFQ
ingest_config("MaxQuant", "proteins", action = "set",
              column_defined = "abundance_raw", column_import = "^LFQ intensity\\s")
}