multi_net_build: Multi-omics network build

In MetaNet: Network Analysis for Omics Data

Multi-omics network build

Description

Multi-omics network build

Usage

multi_net_build(
  ...,
  mode = "full",
  method = "spearman",
  filename = FALSE,
  p.adjust.method = NULL,
  r_threshold = 0.6,
  p_threshold = 0.05,
  use_p_adj = TRUE,
  delete_single = TRUE
)

Arguments

...	some omics abundance tables
mode	"full"
method	"spearman" or "pearson"
filename	the prefix of saved .corr file or FALSE
p.adjust.method	see p.adjust
r_threshold	r_threshold (default: >0.6)
p_threshold	p_threshold (default: <0.05)
use_p_adj	use the p.adjust instead of p-value (default: TRUE)
delete_single	should delete single vertexes?

Value

metanet

See Also

Other build: c_net_build(), c_net_from_edgelist(), c_net_set(), c_net_update()

Examples

data("multi_test")
multi1 <- multi_net_build(list(Microbiome = micro, Metabolome = metab, Transcriptome = transc))
multi1 <- c_net_set(multi1, micro_g, metab_g, transc_g,
  vertex_class = c("Phylum", "kingdom", "type")
)
multi1 <- c_net_set(multi1, data.frame("Abundance1" = colSums(micro)),
  data.frame("Abundance2" = colSums(metab)), data.frame("Abundance3" = colSums(transc)),
  vertex_size = paste0("Abundance", 1:3)
)
c_net_plot(multi1)

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