summary.OpenStatsFE: Summary for an OpenStatsFE object

In mpi2/OpenStats: A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

Summary for an OpenStatsFE object

Description

This function provides summary for an OpenStatsFE object

Usage

 ## S3 method for class 'OpenStatsFE'
summary(object, format = "rst", ...)

Arguments

object	an instance of OpenStatsFE result from OpenStatsAnalysis(method = 'FE') function
format	See format argument from the knitr::kable function
...	Other parameters that can be passed to knitr::kable function

Value

The output consists of the following statistics:

- Applied model
- Checked/optimised model
- Treatment group
- Control group
- If possible, whether sexual dimorphism is detected from the analysis
- Genotype effect p-value
- Genotype effect p-value for females
- Genotype effect p-value for males
- If LifeStage existed in the data, LifeStage p-value
- Genotype effect for early adults
- Genotype effect for late adults
- If Sex existed in the data, Sex p-value
- If bodyweight existed in the data, bodyweight p-value

Author(s)

Hamed Haseli Mashhadi <[e-mail]>

See Also

OpenStatsAnalysis, summary.OpenStatsMM, summary.OpenStatsRR

Examples

####################################################################
# Data preparation
####################################################################
#################
# Categorical data - Creating OpenStatsList object
#################
fileCat <- system.file("extdata", "test_categorical.csv", package = "OpenStats")
test_Cat <- OpenStatsList(
  dataset = read.csv(fileCat, na.strings = "-"),
  testGenotype = "Aff3/Aff3",
  refGenotype = "+/+",
  dataset.colname.genotype = "Genotype",
  dataset.colname.batch = "Assay.Date",
  dataset.colname.lifestage = NULL,
  dataset.colname.weight = "Weight",
  dataset.colname.sex = "Sex"
)
#################
# Fisher's exact test framework
#################
FE_result <- OpenStatsAnalysis(
  OpenStatsList = test_Cat,
  method = "FE",
  FE_formula = Thoracic.Processes ~ Genotype + Sex
)
summary(FE_result)

mpi2/OpenStats documentation built on Sept. 17, 2022, 3:58 p.m.