inferTissue: inferTissue infers the tissue of a single sample (as...

In zwdzwd/sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips

inferTissue infers the tissue of a single sample (as identified through the branchIDs in the row data of the reference) by reporting independent composition through cell type deconvolution.

Description

inferTissue infers the tissue of a single sample (as identified through the branchIDs in the row data of the reference) by reporting independent composition through cell type deconvolution.

Usage

inferTissue(
  betas,
  reference = NULL,
  platform = NULL,
  abs_delta_beta_min = 0.3,
  auc_min = 0.99,
  coverage_min = 0.8,
  topN = 15
)

Arguments

betas	Named vector with probes and their corresponding beta value measurement
reference	Summarized Experiment with either hypomethylated or hypermethylated probe selection (row data), sample selection (column data), meta data, and the betas (assay)
platform	String representing the array type of the betas and reference
abs_delta_beta_min	Numerical value indicating the absolute minimum required delta beta for the probe selection criteria
auc_min	Numeric value corresponding to the minimum AUC value required for a probe to be considered
coverage_min	Numeric value corresponding to the minimum coverage requirement for a probe to be considered. Coverage is defined here as the proportion of samples without an NA value at a given probe.
topN	number of probes to at most use for each branch

Value

inferred tissue as a string

Examples

sesameDataCache() # if not done yet
sdf <- sesameDataGet("MM285.1.SigDF")
inferTissue(getBetas(dyeBiasNL(noob(sdf))))

sesameDataGet_resetEnv()

zwdzwd/sesame documentation built on April 28, 2024, 12:48 p.m.