automatic.COTAN.object.creation: automatic.COTAN.object.creation

In seriph78/COTAN_stable: COexpression Tables ANalysis

Description

automatic.COTAN.object.creation

Usage

automatic.COTAN.object.creation(
  df,
  out_dir,
  GEO,
  sc.method,
  cond,
  mt = FALSE,
  mt_prefix = "^mt",
  cores = 1
)

## S4 method for signature 'data.frame'
automatic.COTAN.object.creation(
  df,
  out_dir,
  GEO,
  sc.method,
  cond,
  mt = FALSE,
  mt_prefix = "^mt",
  cores = 1
)

Arguments

df	dataframe with the row counts
out_dir	directory for the output
GEO	GEO or other code that identify the dataset
sc.method	Type of single cell RNA-seq method used
cond	A string that will identify the sample or condition. It will be part of the final file name.
mt	A boolean (default F). If T mitochondrial genes will be kept in the analysis, otherwise they will be removed.
mt_prefix	is the prefix that identify the mitochondrial genes (default is the mouse prefix: "^mt")
cores	number of cores to be used

Value

It return the COTAN object. It will also store it directly in the output directory

Examples

data("raw.dataset")
obj = automatic.COTAN.object.creation(df= raw,
out_dir =  tempdir(),
GEO = "test_GEO",
sc.method = "test_method",
cond = "test")

seriph78/COTAN_stable documentation built on Dec. 23, 2021, 12:19 a.m.