print.OpenStatsMM: Summary for an OpenStatsMM object

Description Usage Arguments Value Author(s) See Also Examples

View source: R/Prints.R

Description

This function prints summary table for an OpenStatsMM object

Usage

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 ## S3 method for class 'OpenStatsMM'
print(x, format = "rst", ...)

Arguments

x

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 <hamedhm@ebi.ac.uk>

See Also

OpenStatsAnalysis, print.OpenStatsFE, print.OpenStatsRR

Examples

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####################################################################
# 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
)
print(MM1_result)

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