get.analyte.scores: Get features from a SPEAR object.

In jgygi/SPEAR: SPEAR - Sparse Supervised Bayesian Factor Model for Multi-omic Analyses

Get features from a SPEAR object.

Description

Get features from a SPEAR object.

Usage

get.analyte.scores(
  rank = "probability",
  factors = NULL,
  assays = NULL,
  coefficient.cutoff = 0,
  probability.cutoff = 0.95,
  correlation = "none",
  simplify = TRUE
)

Arguments

rank	How to rank features? Defaults to '"probability"' (joint.probability) followed by projection.coefficient. Can also be "'coefficient'" (only projection.coefficient magnitude).
factors	Which factors to return features for? Accepts integers (i.e. 'factors = c(1,2,4)' or 'factors = 1') Defaults to 'NULL' (all).
assays	Which assays? Check names via 'names(SPEAR$data$train)'. Defaults to 'NULL' (all)
coefficient.cutoff	What projection.coefficient value to use as the cutoff? Defaults to 0
probability.cutoff	What joint.probability value to use as the cutoff? Defaults to .95
correlation	Return columns with factor score correlations? Accepts '"spearman"', '"pearson"', '"kendall"', or "'none'" (default)
simplify	Simplify data.frame output to only include Factor, Analyte, Assay, joint.probability and projection.coefficient? Defaults to 'TRUE'

jgygi/SPEAR documentation built on July 5, 2023, 5:35 p.m.