netvis: Visualize differential protein complex co-expression network

In ymatts/RoDiCE: Robust differential co-expression test by copula

Description

Create a plot of differential co-expressed proteins within a complex.

Usage

netvis(obj = NULL, tbl = NULL, ref = NULL, title = NULL, p = 0.05)

Arguments

obj	data.frame. Direct result object of 'coptest.p'.
tbl	data.frame. Alternative with 'obj' when you manually prepare the table. This table must include variables three variables;'varname'(pairs of variable which is separated by '|'), 'stat'(test statistic), 'p'(p-value), and 'p.adj'(adjusted p-value).
ref	data.frame. Group information of the variables, e.g., protein complex. The table must include 'group_id'(group identifier, e,g., protein complex identifier),'desc'(description of the group,e.g., protein complex name),and 'varname'(variable name, e.g., proteins)
title	character. Main title of the plot. if 'ref' is provided, 'title' is set to 'desc'.
p	Single numeric. Significance level for two sample test. The default is 0.05.

Value

Interactive network.

Author(s)

Yusuke Matsui

Yusuke MATSUI

References

Yusuke MATSUI et al.(2020) RoDiCE: Robust differential protein co-expression analysis for cancer complexome (submitted).

Yusuke MATSUI et al.(2020) RoDiCE: Robust differential protein co-expression analysis for cancer complexome (submitted).

Examples

data(ccrcc.pbaf) # example data from clear renal cell carcinoma(clerk et al.2019)
data(corum.hsp.pbaf)
tumor = ccrcc.pbaf$tumor # 110 samples and 10 proteins from PBAF complex
normal = ccrcc.pbaf$normal # 84 samples and 10 proteins from PBAF complex

#perform copula test for pairwise variables.
result = coptest.p(tumor,normal,nperm=100,approx=TRUE)
result$tbl

# without reference
netvis(result,title="PBAF complex")

# with reference
data(corum.hsp.pbaf) # protein complex (PBAF complex; id=149) membership from CORUM database.
netvis(result,ref=corum.hsp.pbaf)

ymatts/RoDiCE documentation built on Jan. 1, 2021, 1:45 p.m.