print.OpenStatsFE: Print summary table for an OpenStatsFE object

Description Usage Arguments Value Author(s) See Also Examples

View source: R/Prints.R

Description

This function prints summary table for an OpenStatsFE object

Usage

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

Arguments

x

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 <hamedhm@ebi.ac.uk>

See Also

OpenStatsAnalysis, print.OpenStatsMM, print.OpenStatsRR

Examples

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####################################################################
# 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
)
print(FE_result)

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