make_fq_dt: make_fq_dt

In FrietzeLabUVM/ssvQC: QC for enrichment based NGS

make_fq_dt

Description

make_fq_dt

Usage

make_fq_dt(
  fastq_files,
  fastq_names = basename(fastq_files),
  fastq_treatments = fastq_names,
  n_cores = getOption("mc.cores", 1),
  cache_counts = TRUE
)

Arguments

fastq_files	paths to fast files (can be gzipped with .gz extension)
fastq_names	optional parallel vector of names for fastq files. Defaults to basename of fastq_files. Should be unique.
fastq_treatments	optional parallel vector of treatments. Defaults to fastq_names. May be duplicated.
n_cores	number of cores to use to count lines in fastq files. Defaults to mc.cores if set or 1.
cache_counts	logical. Should the counts be saved to *.cnt files alongside the fastq_files? Default is TRUE

Value

a data.table countaining fastq, count, name, and treatment attributes

Examples

fq_files = dir("inst/extdata", pattern = "(fq$)|(fq.gz$)|(fastq$)|(fastq.gz$)", full.names = TRUE)
 #no idea why this make_fq_dt example won't run
 #make_fq_dt(fq_files,
 #  fastq_names = c("4_reads_fq", "4_reads_gz", "5_reads_fq", "5_reads_gz"),
 #  cache_counts = FALSE)

FrietzeLabUVM/ssvQC documentation built on March 25, 2024, 12:24 a.m.