analyze: Perform automated analysis.

In gwangjinkim/rnaseqeasy: RNAseq standard analysis

Description

Perform automated analysis.

Usage

analyze(
  keys,
  db,
  meta_dir,
  project_name,
  source,
  sep,
  names,
  out_dir,
  alpha = 0.05,
  lFC = 1,
  ks = "12",
  go = "skip",
  goi = NULL
)

Arguments

keys	list of keys for db. Order determines testing!: First element -> "denom", Second element: "num", rest is ""
db	contains key and list of paths (vector of paths) to key files
meta_dir	the directory to which meta file should be written to. Name is generated automatically using project_name and source
project_name	inserted as signifier into meta filename
source	inserted as signifier into meta filename
sep	separator in meta file - tab
names	names to be used instead of keys
out_dir	output directory for the analysis
alpha	p-value for DESeq2 analysis
lFC	log2FoldChange threshold for significance
ks	number of clusters
go	"skip" or don't skip "yes"
goi	gene of interest for iVolcano and iMDS plot svg

Value

nothing

gwangjinkim/rnaseqeasy documentation built on Jan. 18, 2022, 12:25 a.m.