Parse KneadData log file for a single sample as a named vector

'parse_kneaddata_stats' reads a file obtained from running KneadData on a FASTQ file. This file is parsed into a named vector.

Usage

parse_kneaddata_stats(file_path)

Arguments

file_path

String: Path to a locally stored KneadData log file stored in TXT format

Value

A named vector containing a number of read counts at different stages

Details

'parse_kneaddata_stats' does not parse every single item of information within the out_kneaddata.log file, but gathers only the lines with read counts.

Examples

if (FALSE) { # \dontrun{
if(interactive()){
 fpath <- file.path(system.file("extdata",
                                package = "parkinsonsMetagenomicData"),
                    "sample_out_kneaddata.log")
 parse_kneaddata_stats(fpath)
 }
} # }