c_net_calculate: Calculate correlation for one or two t(otutab), or distance...

In MetaNet: Network Analysis for Omics Data

Calculate correlation for one or two t(otutab), or distance for one t(otutab).

Description

Calculate correlation for one or two t(otutab), or distance for one t(otutab).

Usage

c_net_calculate(
  totu,
  totu2 = NULL,
  method = "spearman",
  filename = FALSE,
  p.adjust.method = NULL,
  p.adjust.mode = "all",
  threads = 1,
  verbose = TRUE
)

Arguments

totu	t(otutab), row are samples, column are features.
totu2	t(otutab2) or NULL, row are samples, column are features.
method	"spearman" (default), "pearson", "sparcc", or distance index from vegdist.
filename	the prefix of saved .corr file or FALSE.
p.adjust.method	see p.adjust
p.adjust.mode	see p.adjust.table
threads	threads, default: 1.
verbose	verbose, default: TRUE.

Value

a corr object with 3 elements:

r	default: spearman correlation
p.value	default: p-value of spearman correlation
p.adjust	default p.adjust.method = NULL

See Also

Other calculate: cal_sim(), fast_cor(), input_corr(), p.adjust.table()

Examples

data("otutab", package = "pcutils")
t(otutab) -> totu
c_net_calculate(totu) -> corr
metadata[, 3:10] -> env
c_net_calculate(totu, env) -> corr2

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