inferTissue {sesame} | R Documentation |
inferTissue1 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.
inferTissue( betas, reference = NULL, platform = NULL, abs_delta_beta_min = 0.3, auc_min = 0.99, coverage_min = 0.8, topN = 15 )
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 |
inferred tissue as a string
sesameDataCache("MM285") # if not done yet sdf = sesameDataGet("MM285.1.SigDF") inferTissue(getBetas(dyeBiasNL(noob(sdf))))