trimming.table | R Documentation |
From fastp runs in ORFik alignment process
trimming.table(
trim_folder,
raw_libraries = dir(trim_folder, "\\.json", full.names = TRUE)
)
trim_folder |
folder of trimmed files, only reads fastp .json files. Can be NULL if raw_libraries is defined |
raw_libraries |
character, default:
|
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).
# 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)
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