FeaturePhenotypeCorrelation

This function performs correlation analysis of a specific feature against a phenotype in the metadata. It can use linear mixed models (LMM), simple linear regression (LM), or Pearson correlation. The default regression line of the plot uses linear model

Usage

FeaturePhenotypeCorrelation(
  mmo,
  feature_id,
  phenotype,
  groups,
  model = "lm",
  normalization = "Z",
  outdir = "FeaturePhenotypeCorrelation",
  width = 6,
  height = 6,
  save_output = TRUE
)

Arguments

mmo

The mmo object with feature data and metadata

feature_id

The id of the feature to analyze

phenotype

The name of the phenotype in the metadata

groups

A vector of group names from the metadata containing phenotype data

model

The type of regression model to use. Options are 'lmm' for linear mixed model, 'lm' for simple linear regression, or 'pearson' for Pearson correlation (default: 'lmm')

normalization

The normalization method to use for feature data. Options are 'None', 'Log', 'Meancentered', or 'Z' (default: 'Z')

outdir

The directory to save the output files

width

The width of the output plot in inches (default: 6)

height

The height of the output plot in inches (default: 6)

save_output

A logical value indicating whether to save the output plot (default: TRUE)

Value

A list of the plot and the raw data