msviper: msVIPER
In viper: Virtual Inference of Protein-activity by Enriched Regulon analysis
Description
Usage
Arguments
Value
See Also
Examples
Description
This function performs MAster Regulator INference Analysis
Usage
1
2
3
4
5
Arguments
ges
Vector containing the gene expression signature to analyze, or matrix with columns containing bootstraped signatures
regulon
Object of class regulon
nullmodel
Matrix of genes by permutations containing the NULL model signatures. A parametric approach equivalent to shuffle genes will be used if nullmodel is ommitted.
pleiotropy
Logical, whether correction for pleiotropic regulation should be performed
minsize
Number indicating the minimum allowed size for the regulons
adaptive.size
Logical, whether the weight (likelihood) should be used for computing the regulon size
ges.filter
Logical, whether the gene expression signature should be limited to the genes represented in the interactome
synergy
Number indicating the synergy computation mode: (0) for no synergy computation; (0-1) for establishing the p-value cutoff for individual TFs to be included in the synergy analysis; (>1) number of top TFs to be included in the synergy analysis
level
Integer, maximum level of combinatorial regulation
pleiotropyArgs
list of 5 numbers for the pleotropy correction indicating: regulators p-value threshold, pleiotropic interaction p-value threshold, minimum number of targets in the overlap between pleiotropic regulators, penalty for the pleiotropic interactions and the pleiotropy analysis method, either absolute or adaptive
cores
Integer indicating the number of cores to use (only 1 in Windows-based systems)
verbose
Logical, whether progression messages should be printed in the terminal
Value
A msviper object containing the following components:
- signature
The gene expression signature
- regulon
The final regulon object used
- es
Enrichment analysis results including regulon size, normalized enrichment score and p-value
- param
msviper parameters, including minsize, adaptive.size
See Also
Examples
1
2
3
4
5
data(bcellViper, package="bcellViper")
sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic
dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations
mra <- msviper(sig, regulon, dnull)
plot(mra, cex=.7)
Example output
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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
The following objects are masked from ‘package:base’:
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,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Thu Dec 3 02:27:25 2020
Computing the null model distribution by 100 permutations.
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Thu Dec 3 02:27:27 2020
Computing regulon enrichment with aREA algorithm
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viper documentation built on Nov. 8, 2020, 7:37 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Value See Also Examples
Description
This function performs MAster Regulator INference Analysis
Usage
1 2 3 4 5 |
Arguments
ges |
Vector containing the gene expression signature to analyze, or matrix with columns containing bootstraped signatures |
regulon |
Object of class regulon |
nullmodel |
Matrix of genes by permutations containing the NULL model signatures. A parametric approach equivalent to shuffle genes will be used if nullmodel is ommitted. |
pleiotropy |
Logical, whether correction for pleiotropic regulation should be performed |
minsize |
Number indicating the minimum allowed size for the regulons |
adaptive.size |
Logical, whether the weight (likelihood) should be used for computing the regulon size |
ges.filter |
Logical, whether the gene expression signature should be limited to the genes represented in the interactome |
synergy |
Number indicating the synergy computation mode: (0) for no synergy computation; (0-1) for establishing the p-value cutoff for individual TFs to be included in the synergy analysis; (>1) number of top TFs to be included in the synergy analysis |
level |
Integer, maximum level of combinatorial regulation |
pleiotropyArgs |
list of 5 numbers for the pleotropy correction indicating: regulators p-value threshold, pleiotropic interaction p-value threshold, minimum number of targets in the overlap between pleiotropic regulators, penalty for the pleiotropic interactions and the pleiotropy analysis method, either absolute or adaptive |
cores |
Integer indicating the number of cores to use (only 1 in Windows-based systems) |
verbose |
Logical, whether progression messages should be printed in the terminal |
Value
A msviper object containing the following components:
- signature
The gene expression signature
- regulon
The final regulon object used
- es
Enrichment analysis results including regulon size, normalized enrichment score and p-value
- param
msviper parameters, including
minsize,adaptive.size
See Also
Examples
1 2 3 4 5 | data(bcellViper, package="bcellViper")
sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic
dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations
mra <- msviper(sig, regulon, dnull)
plot(mra, cex=.7)
|
Example output
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
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
The following objects are masked from ‘package:base’:
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,
union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Thu Dec 3 02:27:25 2020
Computing the null model distribution by 100 permutations.
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Thu Dec 3 02:27:27 2020
Computing regulon enrichment with aREA algorithm
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