Description Usage Format Source References Examples
A combined yeast data set with protein-protein interactions and gene expression (dna damage). Gene expression profiles are transformed into links by computing a Pearson correlation for all pairs of genes and treating all correlations above 0.85 as additional links. Number of genes: 1823, number of interactions: 12382, number of gene expression observations: 52, number of total links with PPI and expression links: 15547.
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List of following objects:
PPI data matrix
gene expression profiles data matrix
Vector of gene ids corresponding to indices used in data matrices
Gene expression observation details
pooled matrix of PPI and expression links
PPI data pooled from yeast data sets of [1] and [2]. Dna damage expression set of [3].
Ulitsky, I. and Shamir, R. Identification of functional modules using network topology and high-throughput data. BMC Systems Biology 2007, 1:8.
Nariai, N., Kolaczyk, E. D. and Kasif, S. Probabilistic Protein Function Predition from Heterogenous Genome-Wide Data. PLoS ONE 2007, 2(3):e337.
Gasch, A., Huang, M., Metzner, S., Botstein, D. and Elledge, S. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Mex1p. Molecular Biology of the Cell 2001, 12:2987-3003.
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Loading required package: BiocGenerics
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Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
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anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
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Package 'mclust' version 5.4.7
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: reshape2
netresponse (C) 2008-2020 Leo Lahti et al.
https://github.com/antagomir/netresponse
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