importSequencingSummary: load a sequencing_summary.txt file into memory

In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

Description

importSequencingSummary loads a sequencing_summary.txt file into memory and performs basic sanity checking to ensure that the file is cleaned of potential duplicate headers from aggregation

Usage

importSequencingSummary(seqsum, cache = TRUE, chunksize = 1e+06,
  skip = FALSE)

Arguments

seqsum	is a path to a file
cache	whether the object created should be cached in env
chunksize	the number of reads to parse per iteration block
skip	whether to skip uncompression if file already exists - may cause collisions due to standard sequencing_summary nomenclature

Value

data.frame of observations from the sequencing_summary.txt file provided

Examples

init()
seqsumFile <- system.file("extdata",
    "sequencing_summary.txt.bz2", package = "nanopoRe")
seqsum <- importSequencingSummary(seqsumFile)

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.