summary_reads: Summarise the reads for indel and GC content and produce the...

In thierrygosselin/stackr: Run stacks software pipeline for RADseq analysis inside R

Description

Still in dev, but work nicely. Summarise the reads for indel and GC content and produce the read depth plot

Usage

summary_reads(
  fq.files,
  output.dir = NULL,
  read.depth.plot = TRUE,
  min.coverage.fig = 7L,
  parallel.core = parallel::detectCores() - 1
)

Arguments

fq.files	(character, path) The path to the individual fastq file to check, or the entire fq folder.
output.dir	(path) Write the output in a specific directory. Default: output.dir = NULL, uses the working directory.
read.depth.plot	(logical) To get the interesting summaries on the read content, the function is very close to similar to read_depth_plot, so you can produce it for each sample with minimal cost on time. Default: read.depth.plot = TRUE.
min.coverage.fig	(character, path). Minimum coverage used to draw the color on the figure. Default: min.coverage.fig = 7L.
parallel.core	(integer) Enable parallel execution with the number of threads. Default: parallel.core = parallel::detectCores() - 1.

Value

The function returns the read depth groups plot and the read stats overall and by read depth groups.

Examples

## Not run: 
require(vroom)
sum <- summary_reads(fq.files = "my_fq_folder")

## End(Not run)

thierrygosselin/stackr documentation built on Nov. 11, 2020, 11 a.m.