list_fastq_files: List fastq files

In MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

List fastq files

Description

Useful for targets bioinformatic pipeline.

Usage

list_fastq_files(
  path,
  paired_end = TRUE,
  pattern = "fastq",
  pattern_R1 = "_R1_",
  pattern_R2 = "_R2_",
  nb_files = Inf
)

Arguments

path	path to files (required)
paired_end	do you have paired_end files? (default TRUE)
pattern	a pattern to filter files (passed on to list.files function).
pattern_R1	a pattern to filter R1 files (default "R1")
pattern_R2	a pattern to filter R2 files (default "R2")
nb_files	the number of fastq files to list (default FALSE)

Value

a list of one (single end) or two (paired end) list of files files are sorted by names (default behavior of list.files())

Author(s)

Adrien Taudière

Examples

list_fastq_files(system.file("extdata", package = "MiscMetabar"))
list_fastq_files(system.file("extdata", package = "MiscMetabar"),
  paired_end = FALSE, pattern_R1 = ""
)

MiscMetabar documentation built on June 21, 2025, 5:09 p.m.