RMT_threshold: Get RMT threshold for a correlation matrix

In MetaNet: Network Analysis for Omics Data

Get RMT threshold for a correlation matrix

Description

Get RMT threshold for a correlation matrix

Get RMT threshold for a correlation matrix roughly

Usage

RMT_threshold(
  occor.r,
  out_dir,
  min_threshold = 0.5,
  max_threshold = 0.8,
  step = 0.02,
  gif = FALSE,
  verbose = FALSE
)

rmt(occor.r, min_threshold = 0.5, max_threshold = 0.85, step = 0.01)

Arguments

occor.r	a corr object or a correlation matrix
out_dir	output dir
min_threshold	min_threshold
max_threshold	max_threshold
step	step
gif	render a .gif file?
verbose	verbose

Value

a r-threshold

recommend threshold

References

J. Zhou, Y. Deng, FALSE. Luo, Z. He, Q. Tu, X. Zhi, (2010) Functional Molecular Ecological Networks, doi:10.1128/mBio.00169-10. https://matstat.org/content_en/RMT/RMThreshold_Intro.pdf

Examples

data(otutab, package = "pcutils")
t(otutab) -> totu
c_net_calculate(totu) -> corr
rmt(corr)
# recommend: 0.69
c_net_build(corr, r_threshold = 0.69) -> co_net_rmt

MetaNet documentation built on May 29, 2024, 1:21 a.m.