OpenStatsBuilder: Method "OpenStatsListBuilder"

In OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

Description

Specifying the age in days, this function creates a 'OpenStatsList' object from a 'PhenList' object from Bioconductor PhenStat package.

Usage

OpenStatsListBuilder(
  PhenListobject,
  DOE = NULL,
  DOB = NULL,
  d.threshold = 16 * 7,
  debug = TRUE
 )

Arguments

PhenListobject	Mandatory argument. Instance of the 'PhenList' object from PhenStat package
DOE	Name of the data column for the 'Batch' in the 'PhenList' object. If left NULL then the input 'PhenList' object will be returned. Default NULL
DOB	Name of the data column for the 'date_of_birth' in the 'PhenList' object. If left NULL then the input 'PhenList' object will be returned. Default NULL
d.threshold	The threshold in age (DOE-DOB) to specify LifeStage early/late levels. The function uses as.Date(DOE)-as.Date(DOB) to calculate the age. The default is 16 weeks (16*7 days)
debug	Logical flag. Set to TRUE to see debug messages. Default TRUE

Value

Provided DOE and DOB are not NULL, a 'OpenStatsList' object that is quite similar to 'PhenList' object with an extra column called 'LifeStage' with two levels 'Early' and 'Late'. Otherwise, the output is similar to the input 'PhenList' object.

Author(s)

Hamed Haseli Mashhadi <[e-mail]>

See Also

OpenStatsAnalysis, OpenStatsList

Examples

	file <- system.file("extdata", "test_continuous.csv", package = "OpenStats")
	####################################################################
	# PhenListObject from PhenStat package
	# The R package PhenStats must be installed in prior
	####################################################################
	PhenListObject <- PhenList(
	  dataset = read.csv(file),
	  testGenotype = "experimental",
	  refGenotype = "control",
	  dataset.colname.batch = "date_of_experiment",
	  dataset.colname.genotype = "biological_sample_group",
	  dataset.colname.sex = "sex",
	  dataset.colname.weight = "weight"
	)
	####################################################################
	# OpenStatsList object
	####################################################################
	OpenStatsListBuilder <- OpenStatsListBuilder(
	  PhenListobject = PhenListObject,
	  DOE = "Batch",
	  DOB = "Birth.Date",
	  d.threshold = 99
	)
	plot(OpenStatsListBuilder)
	class(OpenStatsListBuilder)
	rm(OpenStatsListBuilder)

OpenStats documentation built on Nov. 8, 2020, 5:20 p.m.