list_fastq_files {MiscMetabar}

List fastq files

Description

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("extdata")
list_fastq_files("extdata", paired_end = FALSE, pattern_R1 = "")