summariseSeqkitPEReadStats: Summarising statistics of paired-end read sets
In wanyuac/handyR: Handy functions for R programming.

View source: R/bioinf__summariseSeqkitPEReadStats.R

summariseSeqkitPEReadStats

R Documentation

Summarising statistics of paired-end read sets

Description

This function summarises statistics from seqkit for paired-end read sets. To use this function, the input TSV file must be generated using command 'seqkit stats –all'.

Usage

summariseSeqkitPEReadStats(
  tsv,
  header = c("file", "format", "type", "num_seqs", "sum_len", "min_len", "avg_len",
    "max_len", "Q1", "Q2", "Q3", "sum_gap", "N50", "N50_num", "Q20_perc", "Q30_perc",
    "AvgQual", "GC"),
  ref_len = 5e+06,
  ext = ".fastq.gz",
  suf_R = FALSE,
  sort_by_name = "increasing",
  sort_by_depth = NULL
)

Arguments

`tsv`	Tab-delimited output (a TSV file) from command 'seqkit stats'
`header`	Column names matching seqkit stats's output
`ref_len`	Length of the reference genome in base pairs
`ext`	Filename extension of FASTQ files in the input TSV file. For example, '.fastq.gz' or '.fq.gz'.
`suf_R`	A logical value indicating whether 'R' is used in the filename suffices. For instance, suf_R = TRUE when read files are ended with '_R1.fastq.gz' and '_R2.fastq.gz'.
`sort_by_name`	A string with values "decreasing", "increasing (default), or NULL indicating whether the output data frame will be sorted by isolate names in a specific order. This argument overrides "sort_by_depth" if the former is not NULL.
`sort_by_depth`	A string with values "decreasing", "increasing", or NULL (no sorting) indicating whether the output data frame will be sorted in a specific order for sequencing depths and isolate names.