summary.OpenStatsMM: Summary for an OpenStatsMM object

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

Summary for an OpenStatsMM object

Description

This function provides summary for an OpenStatsMM object

Usage

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

Arguments

object	an instance of OpenStatsMM result from OpenStatsAnalysis(method = 'MM') 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.OpenStatsFE, summary.OpenStatsRR

Examples

####################################################################
# Data preparation
####################################################################
#################
# Continuous data - Creating OpenStatsList object
#################
fileCon <- system.file("extdata", "test_continuous.csv", package = "OpenStats")
test_Cont <- OpenStatsList(
  dataset = read.csv(fileCon),
  testGenotype = "experimental",
  refGenotype = "control",
  dataset.colname.genotype = "biological_sample_group",
  dataset.colname.batch = "date_of_experiment",
  dataset.colname.lifestage = NULL,
  dataset.colname.weight = "weight",
  dataset.colname.sex = "sex"
)

#################
#  Optimised Linear Mixed model (MM) framework
#################
MM1_result <- OpenStatsAnalysis(
  OpenStatsList = test_Cont,
  method = "MM",
  MM_fixed = data_point ~ Genotype + Weight
)
summary(MM1_result)

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