| Title: | Network Analysis for Exposomics |
|---|---|
| Description: | Network analysis for exposomics including generation of exposures-metabolites network, metabolites-metabolites network and gatekeeper metabolites discovery for non-targeted high resolution mass spectrometry data. It can be used to discover gatekeepers. |
| Authors: | Miao YU [aut, cre] (ORCID: <https://orcid.org/0000-0002-2804-6014>) |
| Maintainer: | Miao YU <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.1.0 |
| Built: | 2026-10-31 08:45:59 UTC |
| Source: | https://github.com/yufree/enet |
A vector with asthma condition for 1198 samples
data(asthma)data(asthma)
asthma condition for 1198 samples
1 means asthma and 0 means non-asthma. Raw data are from Exposome Data Challenge 2021.
A dataset with 7 exposures from 1198 samples
data(expo)data(expo)
A data frame with 7 rows and 1198 columns:
7 exposures from 1198 samples. Raw data are from Exposome Data Challenge 2021.
Get correlation cutoff by max network clusters
getcf(mat, cutoff = seq(0, 1, 0.02), ...)getcf(mat, cutoff = seq(0, 1, 0.02), ...)
mat |
dataframe with row as feature and column as samples |
cutoff |
correlation coefficient cutoff |
... |
other parameters for 'cor' |
list with cutoff
data(meta) cf <- getcf(t(meta))data(meta) cf <- getcf(t(meta))
Generate exposures-exposures network
geteenet(expo, cutoff = 0.9, nacf = 0.2, e = NULL, name = NULL, ...)geteenet(expo, cutoff = 0.9, nacf = 0.2, e = NULL, name = NULL, ...)
expo |
exposures dataframe with row as exposures/peaks and column as samples |
cutoff |
correlation coefficient cutoff |
nacf |
NA cutoff for exposure, exposure with NA percentage larger than cutoff will be removed and others will be imputed by knn methods, default 0.2 |
e |
value or vector, specific exposure or peak to its export network |
name |
export gml file for Cytoscape |
... |
other parameters for 'cor' |
list with index of exposures clusters, exposures clusters data and edge table
data(expo) ee <- geteenet(expo)data(expo) ee <- geteenet(expo)
Generate metabolites-exposures network
getemnet(meta, expo, cutoffm = 0.9, cutoffe = 0.6, nacf = 0.2, ...)getemnet(meta, expo, cutoffm = 0.9, cutoffe = 0.6, nacf = 0.2, ...)
meta |
metabolites dataframe with row as metabolites/peaks and column as samples |
expo |
exposures dataframe with row as exposures/peaks and column as samples |
cutoffm |
correlation coefficient cutoff for metabolites-metabolites network |
cutoffe |
correlation coefficient cutoff for exposures-exposures network |
nacf |
NA cutoff for exposure, exposure with NA percentage larger than cutoff will be removed and others will be imputed by knn methods, default 0.2 |
... |
other parameters for 'cor' |
list with table of metabolites-exposures, metabolites-exposures network clusters data and edge table
data(expo) data(meta) me <- getemnet(exp(meta),expo)data(expo) data(meta) me <- getemnet(exp(meta),expo)
Gatekeeper discovery
getgk(meta, expo, cutoff = 0.9, multiple = FALSE, ...)getgk(meta, expo, cutoff = 0.9, multiple = FALSE, ...)
meta |
metabolites dataframe with row as metabolites/peaks and column as samples |
expo |
exposures dataframe with row as exposures/peaks and column as samples |
cutoff |
correlation coefficient cutoff for metabolites-metabolites network |
multiple |
logical, only output gatekeeper with multiple exposures |
... |
other parameters for 'cor' |
list with table of metabolites-exposures, metabolites-exposures network clusters data and edge table
data(expo) data(meta) gk <- getgk(exp(meta),expo)data(expo) data(meta) gk <- getgk(exp(meta),expo)
Generate metabolites-metabolites network
getmmnet(meta, cutoff = 0.9, m = NULL, name = NULL, ...)getmmnet(meta, cutoff = 0.9, m = NULL, name = NULL, ...)
meta |
metabolites dataframe with row as metabolites/peaks and column as samples |
cutoff |
correlation coefficient cutoff |
m |
value or vector, specific metabolite or peak to its export network |
name |
export gml file for Cytoscape |
... |
other parameters for 'cor' |
list with index of metabolites clusters, metabolites clusters data and edge table
data(meta) mm <- getmmnet(meta)data(meta) mm <- getmmnet(meta)
A dataset 177 peaks/metabolites from 1198 samples
data(meta)data(meta)
A data frame with 177 rows and 1198 columns:
177 peaks/metabolites from 1198 samples. Raw data are from Exposome Data Challenge 2021.