trimming.table: Create trimming table

In Roleren/ORFik: Open Reading Frames in Genomics

Create trimming table

Description

From fastp runs in ORFik alignment process

Usage

trimming.table(
  trim_folder,
  raw_libraries = dir(trim_folder, "\\.json$", full.names = TRUE),
  include_adapter = FALSE
)

Arguments

trim_folder	folder of trimmed files, only reads fastp .json files. Can be NULL if raw_libraries is defined
raw_libraries	character, default: dir(trim_folder, "\.json", full.names = TRUE), file paths of all json file paths.
include_adapter	logical, default FALSE. If TRUE, will add an extra column: adapter, with adapter found. If not found, it will specify: "passed".

Value

a data.table with 6 columns, raw_library (names of library), raw_reads (numeric, number of raw reads), trim_reads (numeric, number of trimmed reads), raw_mean_length (numeric, raw mean read length), trim_mean_length (numeric, trim mean read length). Optional columns: adapter (character, adapter, if not found "passed")

Examples

# Location of fastp trimmed .json files
trimmed_file <- system.file("extdata/test_processing/trim",
 "output_template.json", package = "ORFik")
trimmed_folder <- dirname(trimmed_file)
trimming.table(trimmed_folder)
trimming.table(NULL, trimmed_file)
trimming.table(NULL, trimmed_file, include_adapter = TRUE)

Roleren/ORFik documentation built on April 12, 2025, 5:31 a.m.