simpleDecomp: Main PLIER function

In wgmao/PLIER: Pathway-Level Information Extractor (PLIER): a generative model for gene expression data

Main PLIER function

Description

Main PLIER function

Usage

simpleDecomp(
  Y,
  k,
  svdres = NULL,
  L1 = NULL,
  L2 = NULL,
  max.iter = 200,
  tol = 5e-06,
  trace = F,
  rseed = NULL,
  B = NULL,
  scale = 1,
  adaptive.frac = 0.05,
  adaptive.iter = 30
)

Arguments

k	The number of latent variables to return, leave as NULL to be set automatically using the num.pc "elbow" method
svdres	Pre-computed result of the svd decomposition for data.
L1	L1 constant, leave as NULL to automatically select a value.
L2	L2 constant, leave as NULL to automatically select a value.
max.iter	maximum number of iterations, default is 200.
tol	tolerance for relative B change, default is 5e-6.
trace	print out trace info, default is false.
rseed	seed for RSVD call. If svdres us given this has no effect.
adaptive.frac	the probability cutoff to use to determine the positive cutoff for loading. Smaller values will return sparser models.
adaptive.iter	the first iteration where adaptive constants are computed, before they are all 0.
data	the data to be processed with genes in rows and samples in columns. Should be z-scored.
scaleL	scale both L1 and L2 by this amount from the default setting. Values less then 1 imply weaker regularization.

wgmao/PLIER documentation built on Sept. 1, 2024, 10:25 p.m.