| Title: | Virtual Inference of Protein-activity by Enriched Regulon analysis |
|---|---|
| Description: | Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms |
| Authors: | Mariano J Alvarez <[email protected]> |
| Maintainer: | Mariano J Alvarez <[email protected]> |
| License: | file LICENSE |
| Version: | 1.39.0 |
| Built: | 2024-07-16 05:14:30 UTC |
| Source: | https://github.com/bioc/viper |
This function generates an empirical null model that computes a normalized statistics and p-value
aecdf(dnull, symmetric = FALSE, n = 100)aecdf(dnull, symmetric = FALSE, n = 100)
dnull |
Numerical vector representing the null model |
symmetric |
Logical, whether the distribution should betreated as symmetric around zero and only one tail should be approximated |
n |
Integer indicating the number of points to evaluate the empirical cummulative probability function |
function with two parameters, x and alternative
This function uses a gaussian kernel to estimate the joint density distribution at the specified points
approxk2d(x, gridsize = 128, pos = x)approxk2d(x, gridsize = 128, pos = x)
x |
Matrix of x and y points |
gridsize |
number or vector indicating the size of the greed where to estimate the density |
pos |
Matrix of coordinates to evaluate the density |
Vector of density estimates
x <- rnorm(500) y <- x+rnorm(500) kde2 <- approxk2d(cbind(x, y)) plot(x, y, pch=20, col=hsv(0, kde2/max(kde2), 1))x <- rnorm(500) y <- x+rnorm(500) kde2 <- approxk2d(cbind(x, y)) plot(x, y, pch=20, col=hsv(0, kde2/max(kde2), 1))
This function generates a regulon object from ARACNe results and the corresponding expression dataset
aracne2regulon(afile, eset, gene = FALSE, format = c("adj", "3col"), verbose = TRUE)aracne2regulon(afile, eset, gene = FALSE, format = c("adj", "3col"), verbose = TRUE)
afile |
Character string indicating the name of the ARACNe network file |
eset |
Either a character string indicating the name of the expression-dataset file, a ExpressionSet object or a gene expression matrix with genes (probes) in rows and samples in columns |
gene |
Logical, whether the probes should be collapsed at the gene level |
format |
Character string, indicating the format of the aracne file, either adj for adjacency matrixes generated by aracne, or 3col when the interactome is represented by a 3 columns text file, with regulator in the first column, target in the second and mutual information in the third column |
verbose |
Logical, whether progression messages should be printed in the terminal. |
Regulon object
data(bcellViper, package="bcellViper") adjfile <- file.path(find.package("bcellViper"), "aracne", "bcellaracne.adj") regul <- aracne2regulon(adjfile, dset) print(regul)data(bcellViper, package="bcellViper") adjfile <- file.path(find.package("bcellViper"), "aracne", "bcellaracne.adj") regul <- aracne2regulon(adjfile, dset) print(regul)
This function generates a regulon object from ARACNe results and the corresponding expression dataset when correction for CNV have been applied
aracne2regulon4cnv(afile, eset, regeset, gene = FALSE, format = c("adj", "3col"), verbose = TRUE)aracne2regulon4cnv(afile, eset, regeset, gene = FALSE, format = c("adj", "3col"), verbose = TRUE)
afile |
Character string indicating the name of the ARACNe network file |
eset |
Either a character string indicating the name of the expression-dataset file, a ExpressionSet object or a gene expression matrix with genes (probes) in rows and samples in columns, where the expression was corrected by CNV |
regeset |
Either a character string indicating the name of the expression-dataset file, a ExpressionSet object or a gene expression matrix with genes (probes) in rows and samples in columns |
gene |
Logical, whether the probes should be collapsed at the gene level |
format |
Character string, indicating the format of the aracne file, either adj for adjacency matrixes generated by aracne, or 3col when the interactome is represented by a 3 columns text file, with regulator in the first column, target in the second and mutual information in the third column |
verbose |
Logical, whether progression messages should be printed in the terminal. |
Regulon object
data(bcellViper, package="bcellViper") adjfile <- file.path(find.package("bcellViper"), "aracne", "bcellaracne.adj") regul <- aracne2regulon(adjfile, dset) print(regul)data(bcellViper, package="bcellViper") adjfile <- file.path(find.package("bcellViper"), "aracne", "bcellaracne.adj") regul <- aracne2regulon(adjfile, dset) print(regul)
This function performs wREA enrichment analysis on a set of signatues
aREA(eset, regulon, method = c("auto", "matrix", "loop"), minsize = 20, cores = 1, wm = NULL, verbose = FALSE)aREA(eset, regulon, method = c("auto", "matrix", "loop"), minsize = 20, cores = 1, wm = NULL, verbose = FALSE)
eset |
Matrix containing a set of signatures, with samples in columns and traits in rows |
regulon |
Regulon object |
method |
Character string indicating the implementation, either auto, matrix or loop |
minsize |
Interger indicating the minimum allowed size for the regulons |
cores |
Integer indicating the number of cores to use (only 1 in Windows-based systems) |
wm |
Optional numeric matrix of weights (0; 1) with same dimension as eset |
verbose |
Logical, whether a progress bar should be shown |
List of two elements, enrichment score and normalized enrichment score
This function transforms a signatureDistance object into a dist object
## S3 method for class 'signatureDistance' as.dist(m, diag = FALSE, upper = FALSE)## S3 method for class 'signatureDistance' as.dist(m, diag = FALSE, upper = FALSE)
m |
signatureDistance object |
diag |
parameter included for compatibility |
upper |
parameter included for compatibility |
Object of class dist
This function integrates the bootstrap msviper results
bootstrapmsviper(mobj, method = c("mean", "median", "mode"))bootstrapmsviper(mobj, method = c("mean", "median", "mode"))
mobj |
msviper object |
method |
Character string indicating the method to use, either mean, median or mode |
msviper object
data(bcellViper, package="bcellViper") sig <- bootstrapTtest(dset, "description", c("CB", "CC"), "N") mra <- msviper(sig, regulon) plot(mra, cex=.7)data(bcellViper, package="bcellViper") sig <- bootstrapTtest(dset, "description", c("CB", "CC"), "N") mra <- msviper(sig, regulon) plot(mra, cex=.7)
This function generates a bootstrapped signature matrix by t-test
bootstrapTtest(x, ...) ## S4 method for signature 'matrix' bootstrapTtest(x, y, per = 100, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'ExpressionSet' bootstrapTtest(x, pheno, group1, group2, per = 100, seed = 1, verbose = TRUE)bootstrapTtest(x, ...) ## S4 method for signature 'matrix' bootstrapTtest(x, y, per = 100, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'ExpressionSet' bootstrapTtest(x, pheno, group1, group2, per = 100, seed = 1, verbose = TRUE)
x |
Matrix containing the test dataset |
... |
Additional parameters added to keep compatibility |
y |
Matrix containing the reference dataset |
per |
Integer indicating the number of permutations |
seed |
Integer indicating the seed for the permutations, 0 for disable it |
cores |
Integer indicating the number of cores to use (set to 1 in Windows-based systems) |
verbose |
Logical whether progress should be reported |
pheno |
Character string indicating the phenotype data to use |
group1 |
Vector of character strings indicating the category from phenotype |
group2 |
Vector of character strings indicating the category from phenotype |
Matrix of z-scores with genes in rows and permutations in columns
data(bcellViper, package="bcellViper") d1 <- exprs(dset) sig <- bootstrapTtest(d1[, 1:10], d1[, 11:20], per=100) dim(sig) plot(density(sig[1907, ])) data(bcellViper, package="bcellViper") sig <- bootstrapTtest(dset, "description", "CB", "N", per=100) dim(sig) plot(density(sig[1907, ]))data(bcellViper, package="bcellViper") d1 <- exprs(dset) sig <- bootstrapTtest(d1[, 1:10], d1[, 11:20], per=100) dim(sig) plot(density(sig[1907, ])) data(bcellViper, package="bcellViper") sig <- bootstrapTtest(dset, "description", "CB", "N", per=100) dim(sig) plot(density(sig[1907, ]))
This function performs a viper analysis with bootstraps
bootstrapViper(eset, regulon, nes = TRUE, bootstraps = 10, eset.filter = FALSE, adaptive.size = TRUE, minsize = 20, mvws = 1, cores = 1, verbose = TRUE)bootstrapViper(eset, regulon, nes = TRUE, bootstraps = 10, eset.filter = FALSE, adaptive.size = TRUE, minsize = 20, mvws = 1, cores = 1, verbose = TRUE)
eset |
ExpressionSet object or Numeric matrix containing the expression data, with samples in columns and genes in rows |
regulon |
Object of class regulon |
nes |
Logical, whether the enrichment score reported should be normalized |
bootstraps |
Integer indicating the number of bootstraps iterations to perform. Only the scale method is implemented with bootstraps. |
eset.filter |
Logical, whether the dataset should be limited only to the genes represented in the interactome |
adaptive.size |
Logical, whether the weighting scores should be taken into account for computing the regulon size |
minsize |
Integer indicating the minimum number of targets allowed per regulon |
mvws |
Number or vector indicating either the exponent score for the metaViper weights, or the inflection point and trend for the sigmoid function describing the weights in metaViper |
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 |
A list containing a matrix of inferred activity for each regulator gene in the network across all samples and the corresponding standard deviation computed from the bootstrap iterations.
data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- viper(d1[, 1:50], regulon, bootstraps=10) # Run only on 50 samples to reduce computation time dim(d1) d1[1:5, 1:5] regulon dim(res$nes) res$nes[1:5, 1:5] res$sd[1:5, 1:5]data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- viper(d1[, 1:50], regulon, bootstraps=10) # Run only on 50 samples to reduce computation time dim(d1) d1[1:5, 1:5] regulon dim(res$nes) res$nes[1:5, 1:5] res$sd[1:5, 1:5]
This function convers combinatorial annotations
comNames(x, annot)comNames(x, annot)
x |
Character vector of gene name combinations, where the combinations are separated by – |
annot |
Vector of gene names with geneID as |
Converted annotations
This function computes the mode for continuous distributions
distMode(x, adj = 1)distMode(x, adj = 1)
x |
Numeric data vector |
adj |
Number indicating the adjustment for the kernel bandwidth |
Number
data(bcellViper, package="bcellViper") d1 <- exprs(dset) mean(d1[, 1]) median(d1[, 1]) distMode(d1[, 1]) plot(density(d1[, 1])) abline(v=c(mean(d1[, 1]), median(d1[, 1]), distMode(d1[, 1])), col=c("green", "red", "blue")) legend("topleft", c("Mean", "Median", "Mode"), col=c("green", "red", "blue"), lwd=4)data(bcellViper, package="bcellViper") d1 <- exprs(dset) mean(d1[, 1]) median(d1[, 1]) distMode(d1[, 1]) plot(density(d1[, 1])) abline(v=c(mean(d1[, 1]), median(d1[, 1]), distMode(d1[, 1])), col=c("green", "red", "blue")) legend("topleft", c("Mean", "Median", "Mode"), col=c("green", "red", "blue"), lwd=4)
This function computes the variance by columns ignoring NA values
fcvarna(x)fcvarna(x)
x |
Numeric matrix |
1-column matrix with the variance by column results
data(bcellViper, package="bcellViper") tmp <- exprs(dset)[, 1:10] tmp[round(runif(100, 1, length(tmp)))] <- NA fcvarna(tmp)data(bcellViper, package="bcellViper") tmp <- exprs(dset)[, 1:10] tmp[round(runif(100, 1, length(tmp)))] <- NA fcvarna(tmp)
This function filters the columns of a matrix returning always a two dimensional matrix
filterColMatrix(x, filter)filterColMatrix(x, filter)
x |
Matrix |
filter |
Logical or numerical index of columns |
Matrix
This function filter redundant probes based on the highest coefficient of variation
filterCV(expset, ...) ## S4 method for signature 'matrix' filterCV(expset) ## S4 method for signature 'ExpressionSet' filterCV(expset)filterCV(expset, ...) ## S4 method for signature 'matrix' filterCV(expset) ## S4 method for signature 'ExpressionSet' filterCV(expset)
expset |
Expression set or Matrix containing the gene expression data, with samples in columns and probes in rows. The |
... |
Additional parameters added to keep compatibility |
CV filtered dataset
data(bcellViper, package="bcellViper") d1 <- exprs(dset) tmp <- rownames(d1) tmp[round(runif(10, 1, length(tmp)))] <- tmp[1] rownames(d1) <- tmp dim(d1) d1 <- filterCV(d1) dim(d1)data(bcellViper, package="bcellViper") d1 <- exprs(dset) tmp <- rownames(d1) tmp[round(runif(10, 1, length(tmp)))] <- tmp[1] rownames(d1) <- tmp dim(d1) d1 <- filterCV(d1) dim(d1)
This function filters the rows of a matrix returning always a two dimensional matrix
filterRowMatrix(x, filter)filterRowMatrix(x, filter)
x |
Matrix |
filter |
Logical or numerical index of rows |
Matrix
This function computes the coefficient of variation (CV) by rows
frcv(x)frcv(x)
x |
Numeric matrix |
1-column matrix with the coefficient of variation by row results
data(bcellViper, package="bcellViper") tmp <- exprs(dset)[1:10, ] tmp[round(runif(100, 1, length(tmp)))] <- NA frcv(tmp)data(bcellViper, package="bcellViper") tmp <- exprs(dset)[1:10, ] tmp[round(runif(100, 1, length(tmp)))] <- NA frcv(tmp)
This function computes the variance by rows ignoring NA values
frvarna(x)frvarna(x)
x |
Numeric matrix |
1-column matrix with the variance by row results
data(bcellViper, package="bcellViper") tmp <- exprs(dset)[1:10, ] tmp[round(runif(100, 1, length(tmp)))] <- NA frvarna(tmp)data(bcellViper, package="bcellViper") tmp <- exprs(dset)[1:10, ] tmp[round(runif(100, 1, length(tmp)))] <- NA frvarna(tmp)
This function performs a Proportionally Weighted Enrichment Analysis on groups of gene-sets
groupPwea3(rlist, groups, nullpw = NULL, alternative = c("two.sided", "less", "greater"), per = 0, minsize = 5, cores = 1, verbose = TRUE)groupPwea3(rlist, groups, nullpw = NULL, alternative = c("two.sided", "less", "greater"), per = 0, minsize = 5, cores = 1, verbose = TRUE)
rlist |
Named vector containing the scores to rank the expression profile or matrix where columns contains bootstraped signatures |
groups |
List of gene-sets (regulons), each component is a list of two vectors: TFmode containing the TFMoA index (-1; 1) and likelihood containing the interaction relative likelihood |
nullpw |
Numerical matrix representing the null model, with genes as rows (geneID as rownames) and permutations as columns |
alternative |
Character string indicating the alternative hypothesis, either two.sided, greater or less |
per |
Integer indicating the number of permutations for the genes in case "nullpw" is ommited |
minsize |
Integer indicating the minimum size for the regulons |
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 |
A list containing four matrices:
Enrichment score
Normalized Enrichment Score
Regulon size
Enrichment p.value
This function integrates signatures represented as columns in the input matrix using self-weighting average
integrateSignatures(signature, score = 1)integrateSignatures(signature, score = 1)
signature |
Numeric matrix containing the signatures as z-scores or NES, genes in rows and signatures in columns |
score |
Number indicating the exponent score for the weight |
Vector containing the integrated signatures
data(bcellViper, package="bcellViper") sig <- bootstrapTtest(dset, "description", "CB", "N", per=100) isig <- integrateSignatures(sig) plot(density(sig)) lines(density(isig, adj=1.5), col="red")data(bcellViper, package="bcellViper") sig <- bootstrapTtest(dset, "description", "CB", "N", per=100) isig <- integrateSignatures(sig) plot(density(sig)) lines(density(isig, adj=1.5), col="red")
This function performs a Leading-Edge analysis on an object of class msviper
ledge(mobj)ledge(mobj)
mobj |
msviper class object |
msviper object updated with a ledge slot
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", "CB", "N")$statistic mra <- msviper(sig, regulon) mra <- ledge(mra) summary(mra)data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", "CB", "N")$statistic mra <- msviper(sig, regulon) mra <- ledge(mra) summary(mra)
This function load an expression file into a matrix
loadExpset(filename)loadExpset(filename)
filename |
Character string indicating the name of the expression file |
List containing a numeric matrix of expression data with samples in columns and probes in rows; and a vector of gene mapping annotations
This function performs MAster Regulator INference Analysis
msviper(ges, regulon, nullmodel = NULL, pleiotropy = FALSE, minsize = 25, adaptive.size = FALSE, ges.filter = TRUE, synergy = 0, level = 10, pleiotropyArgs = list(regulators = 0.05, shadow = 0.05, targets = 10, penalty = 20, method = "adaptive"), cores = 1, verbose = TRUE)msviper(ges, regulon, nullmodel = NULL, pleiotropy = FALSE, minsize = 25, adaptive.size = FALSE, ges.filter = TRUE, synergy = 0, level = 10, pleiotropyArgs = list(regulators = 0.05, shadow = 0.05, targets = 10, penalty = 20, method = "adaptive"), cores = 1, verbose = TRUE)
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 |
A msviper object containing the following components:
The gene expression signature
The final regulon object used
Enrichment analysis results including regulon size, normalized enrichment score and p-value
msviper parameters, including minsize, adaptive.size
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations mra <- msviper(sig, regulon, dnull) plot(mra, cex=.7)data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$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)
This class contains the results generated by the msviper function
signature:Matrix containing the gene expression signature
regulon:Object of class regulon
es:List containing 6 objects:
es$es:Named vector of class numeric containing the enrichment scores
es$nes:Named vector of class numeric containing the normalized enrichment scores
es$nes.se:Named vector of class numeric containing the standard error for the normalized enrichment score
es$size:Named vector of class numeric containing the size -number of target genes- for each regulator
es$p.value:Named vector of class numeric containing the enrichment p-values
es$nes.bt:Matrix containing the normalized enrichment score if the msviper test is performed with bootstraps
param:List containing 3 elements:
param$minsize:Integer indicating the minimum allowed size for the regulons
param$adaptive.size:Logical indicating whether the weight (likelihood) should be used for computing the regulon size
param$iterative:Logical indicating whether a two step analysis with adaptive redundancy estimation should be performed
nullmodel:Matrix of genes by permutations containing the NULL model signatures
ledge:List containing the leading edge genes for each regulator. This slot is added by the ledge function
shadow:Two columns matrix containing the gene names for the shadow pairs. The first column contain the most probble regulator and the second column the one that was identified because a shadow effect
This function changes the annotation of genes in msviper objects
msviperAnnot(mobj, annot, complete = TRUE)msviperAnnot(mobj, annot, complete = TRUE)
mobj |
msviper object generated by |
annot |
Vector os character strings containing the gene names and gene identifiers as vector names attribute |
complete |
Logical, whether the signature and target names should be also transformed |
msviper object with updated annotations
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", "CB", "N")$statistic mra <- msviper(sig, regulon) tmp <- unique(c(names(mra$regulon), rownames(mra$signature))) annot <- 1:length(tmp) names(annot) <- tmp plot(mra, cex=.7) mra <- msviperAnnot(mra, annot) plot(mra, cex=.7)data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", "CB", "N")$statistic mra <- msviper(sig, regulon) tmp <- unique(c(names(mra$regulon), rownames(mra$signature))) annot <- 1:length(tmp) names(annot) <- tmp plot(mra, cex=.7) mra <- msviperAnnot(mra, annot) plot(mra, cex=.7)
This function generates an instance of the msviper class from a signature, NES signature and regulon object
msviperClass(nes, signature, regulon, nullmodel = NULL)msviperClass(nes, signature, regulon, nullmodel = NULL)
nes |
Numeric vector of NES values |
signature |
Numeric vector of gene expression signature |
regulon |
Instance of class regulon |
nullmodel |
Optional matrix containing the signatures for the null model |
msviper class object
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic mra <- msviper(sig, regulon) mra1 <- msviperClass(mra$es$nes, sig, regulon) summary(mra1) plot(mra1)data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic mra <- msviper(sig, regulon) mra1 <- msviperClass(mra$es$nes, sig, regulon) summary(mra1) plot(mra1)
This function performs combinatorial analysis for msviper objects
msviperCombinatorial(mobj, regulators = 100, nullmodel = NULL, minsize = NULL, adaptive.size = NULL, level = 10, cores = 1, processAll = FALSE, verbose = TRUE)msviperCombinatorial(mobj, regulators = 100, nullmodel = NULL, minsize = NULL, adaptive.size = NULL, level = 10, cores = 1, processAll = FALSE, verbose = TRUE)
mobj |
msviper object generated by |
regulators |
Either a number between 0 and 1 indicating the p-value cutoff for individual TFs to be included in the combinations analysis; (>1) indicating the number of top TFs to be included in the combinations analysis; or a vector of character strings indicating the TF IDs to be included in the analysis |
nullmodel |
Matrix of genes by permutations containing the NULL model signatures. Taken from |
minsize |
Number indicating the minimum allowed size for the regulons, taken from |
adaptive.size |
Logical, whether the weight (likelihood) should be used for computing the size, taken from |
level |
Integer, maximum level of combinatorial regulation |
cores |
Integer indicating the number of cores to use (only 1 in Windows-based systems) |
processAll |
Logical, whether all pairs, even if not significant, should be processed for synergy |
verbose |
Logical, whether progression messages should be printed in the terminal |
A msviper object
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$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) mra <- msviperCombinatorial(mra, 20) plot(mra, cex=.7)data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations mra <- msviper(sig, regulon, dnull) mra <- msviperCombinatorial(mra, 20) plot(mra, cex=.7)
This function performs a synergy analysis for combinatorial regulation
msviperSynergy(mobj, per = 1000, seed = 1, cores = 1, verbose = TRUE)msviperSynergy(mobj, per = 1000, seed = 1, cores = 1, verbose = TRUE)
mobj |
msviper object containing combinatorial regulation results generated by |
per |
Integer indicating the number of permutations |
seed |
Integer indicating the seed for the permutations, 0 for disable it |
cores |
Integer indicating the number of cores to use (only 1 in Windows-based systems) |
verbose |
Logical, whether progression messages should be printed in the terminal |
Updated msviper object containing the sygergy p-value
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$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) mra <- msviperCombinatorial(mra, 20) mra <- msviperSynergy(mra) summary(mra)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) mra <- msviperCombinatorial(mra, 20) mra <- msviperSynergy(mra) summary(mra)
This function generate a plot for msviper results showing the enrichment of the target genes for each significant master regulator on the gene expression signature
## S3 method for class 'msviper' plot(x, mrs = 10, color = c("cornflowerblue", "salmon"), pval = NULL, bins = 500, cex = 0, density = 0, smooth = 0, sep = 0.2, hybrid = TRUE, include = c("expression", "activity"), gama = 2, ...)## S3 method for class 'msviper' plot(x, mrs = 10, color = c("cornflowerblue", "salmon"), pval = NULL, bins = 500, cex = 0, density = 0, smooth = 0, sep = 0.2, hybrid = TRUE, include = c("expression", "activity"), gama = 2, ...)
x |
msviper object produced by |
mrs |
Either an integer indicating the number of master regulators to include in the plot, or a character vector containing the names of the master regulators to include in the plot |
color |
Vector of two components indicating the colors for the negative and positive parts of the regulon |
pval |
Optional matrix of p-values to include in the plot |
bins |
Number of bins to split the vector of scores in order to compute the density color of the bars |
cex |
Number indicating the text size scaling, 0 indicates automatic scaling |
density |
Integrer indicating the number of steps for the kernel density. Zero for not ploting it |
smooth |
Number indicating the proportion of point for smoothing the density distribution. Zero for not using the smoother |
sep |
Number indicating the separation from figure and text |
hybrid |
Logical, whether the 3-tail approach used for computingthe enrichment should be reflected in the plot |
include |
Vector indicating the information to include as heatmap to the right of the msviper plot: expression and activity |
gama |
Positive number indicating the exponential transformation for the activity and expression color scale |
... |
Given for compatibility to the plot generic function |
Nothing, a plot is generated in the default output device
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)data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations mra <- msviper(sig, regulon, dnull) plot(mra, cex=.7)
This function limits the maximum size of the regulons
pruneRegulon(regulon, cutoff = 50, adaptive = TRUE, eliminate = FALSE, wm = NULL)pruneRegulon(regulon, cutoff = 50, adaptive = TRUE, eliminate = FALSE, wm = NULL)
regulon |
Object of class regulon |
cutoff |
Number indicating the maximum size for the regulons (maximum number of target genes) |
adaptive |
Logical, whether adaptive size should be used (i.e. sum(likelihood^2)) |
eliminate |
Logical whether regulons smalles than |
wm |
Optional numeric vector of weights (0; 1) for the genes |
Prunned regulon
data(bcellViper, package="bcellViper") hist(sapply(regulon, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20) preg <- pruneRegulon(regulon, 400) hist(sapply(preg, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20)data(bcellViper, package="bcellViper") hist(sapply(regulon, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20) preg <- pruneRegulon(regulon, 400) hist(sapply(preg, function(x) sum(x$likelihood)/max(x$likelihood)), nclass=20)
This function generates the NULL model function, which computes the normalized enrichment score and associated p-value
pwea3NULLf(pwnull, cores = 1, verbose = TRUE)pwea3NULLf(pwnull, cores = 1, verbose = TRUE)
pwnull |
Object generated by |
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 |
List of function to compute NES and p-value
This function generates the regulon-specific NULL models
pwea3NULLgroups(pwnull, groups, cores = 1, verbose = TRUE)pwea3NULLgroups(pwnull, groups, cores = 1, verbose = TRUE)
pwnull |
Numerical matrix representing the null model, with genes as rows (geneID as rownames) and permutations as columns |
groups |
List containing the regulons |
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 |
A list containing two elements:
Regulon-specific NULL model containing the enrichment scores
Direction of the regulon-specific NULL model
This class contains interactome data
List of regulators with the following slots:
tfmode:Named vector of class numeric containing the regulator mode of action scores, with target genes as name attribute
likelihood:Vector of class numeric containing the relative likelihood for each target gene
This function performs a Student's t-test on each row of a matrix
rowTtest(x, ...) ## S4 method for signature 'matrix' rowTtest(x, y = NULL, mu = 0, alternative = "two.sided") ## S4 method for signature 'ExpressionSet' rowTtest(x, pheno, group1, group2 = NULL, mu = 0, alternative = "two.sided")rowTtest(x, ...) ## S4 method for signature 'matrix' rowTtest(x, y = NULL, mu = 0, alternative = "two.sided") ## S4 method for signature 'ExpressionSet' rowTtest(x, pheno, group1, group2 = NULL, mu = 0, alternative = "two.sided")
x |
ExpressionSet object or Numerical matrix containing the test samples |
... |
Additional parameters added to keep compatibility |
y |
Optional numerical matrix containing the reference samples. If ommited |
mu |
Number indicating the alternative hypothesis when |
alternative |
Character string indicating the tail for the test, either two.sided, greater or lower |
pheno |
Character string indicating the phenotype data to use |
group1 |
Vector of character strings indicating the category from phenotype |
group2 |
Vector of character strings indicating the category from phenotype |
List of Student-t-statistic (statistic) and p-values (p.value)
data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- rowTtest(d1[, 1:10], d1[, 11:20]) res$statistic[1:5, ] res$p.value[1:5, ] data(bcellViper, package="bcellViper") res <- rowTtest(dset, "description", "CB", "N") res$statistic[1:5, ] res$p.value[1:5, ]data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- rowTtest(d1[, 1:10], d1[, 11:20]) res$statistic[1:5, ] res$p.value[1:5, ] data(bcellViper, package="bcellViper") res <- rowTtest(dset, "description", "CB", "N") res$statistic[1:5, ] res$p.value[1:5, ]
This function scales the signatureDistance so its range is (-1, 1)
## S3 method for class 'signatureDistance' scale(x, center = TRUE, scale = TRUE)## S3 method for class 'signatureDistance' scale(x, center = TRUE, scale = TRUE)
x |
signatureDistance object |
center |
Not used, given for compatibility with the generic funtion scale |
scale |
Not used, given for compatibility with the generic function scale |
Scaled signatureDistance object
scaleGroups compares each group vs. the remaining groups using a Student's t-test
scaleGroups(x, groups)scaleGroups(x, groups)
x |
Numerical matrix with genes in rows and samples in columns |
groups |
Vector of same length as columns has the dset containing the labels for grouping the samples |
This function compute signatures using groups information
Numeric matrix of signatures (z-scores) with genes in rows and groups in columns
data(bcellViper, package="bcellViper") res <- scaleGroups(exprs(dset)[, 1:20], rep(1:4, rep(5, 4))) res[1:5, ]data(bcellViper, package="bcellViper") res <- scaleGroups(exprs(dset)[, 1:20], rep(1:4, rep(5, 4))) res[1:5, ]
This function performs shadow analysis on msviper objects
shadow(mobj, regulators = 0.01, targets = 10, shadow = 0.01, per = 1000, nullmodel = NULL, minsize = NULL, adaptive.size = NULL, iterative = NULL, seed = 1, cores = 1, verbose = TRUE)shadow(mobj, regulators = 0.01, targets = 10, shadow = 0.01, per = 1000, nullmodel = NULL, minsize = NULL, adaptive.size = NULL, iterative = NULL, seed = 1, cores = 1, verbose = TRUE)
mobj |
msviper object generated by |
regulators |
This parameter represent different ways to select a subset of regulators for performing the shadow analysis, it can be either a p-value cutoff, the total number of regulons to be used for computing the shadow effect, or a vector of regulator ids to be considered |
targets |
Integer indicating the minimum number of common targets to compute shadow analysis |
shadow |
Number indicating the p-value threshold for the shadow effect |
per |
Integer indicating the number of permutations |
nullmodel |
Null model in marix format |
minsize |
Integer indicating the minimum size allowed for the regulons |
adaptive.size |
Logical, whether the target weight should be considered when computing the regulon size |
iterative |
Logical, whether a two step analysis with adaptive redundancy estimation should be performed |
seed |
Integer indicating the seed for the permutations, 0 for disable it |
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 |
An updated msviper object with an additional slot (shadow) containing the shadow pairs
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) mra <- shadow(mra, regulators=10) summary(mra)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) mra <- shadow(mra, regulators=10) summary(mra)
This function penalyze the regulatory interactions based on pleiotropy analysis
shadowRegulon(ss, nes, regul, regulators = 0.05, shadow = 0.05, targets = 10, penalty = 2, method = c("absolute", "adaptive"))shadowRegulon(ss, nes, regul, regulators = 0.05, shadow = 0.05, targets = 10, penalty = 2, method = c("absolute", "adaptive"))
ss |
Named vector containing the gene expression signature |
nes |
Named vector containing the normalized enrichment scores |
regul |
Regulon object |
regulators |
Number indicating the number of top regulators to consider for the analysis or the p-value threshold for considering significant regulators |
shadow |
Number indicating the p-value threshold for considering a significant shadow effect |
targets |
Integer indicating the minimal number of overlaping targets to consider a pair of regulators for pleiotropy analysis |
penalty |
Number higher than 1 indicating the penalty for the pleiotropic interactions. 1 = no penalty |
method |
Character string indicating the method to use for computing the pleiotropy, either absolute or adaptive |
Corrected regulon object
This function computes the similarity between columns of a data matrix
signatureDistance(dset1, dset2 = NULL, nn = NULL, groups = NULL, scale. = TRUE, two.tails = TRUE, ws = 2)signatureDistance(dset1, dset2 = NULL, nn = NULL, groups = NULL, scale. = TRUE, two.tails = TRUE, ws = 2)
dset1 |
Dataset of any type in matrix format, with features in rows and samples in columns |
dset2 |
Optional Dataset. If provided, distance between columns of dset and dset2 are computed and reported as rows and columns, respectively; if not, distance between all possible pairs of columns from dset are computed |
nn |
Optional size for the signature, default is either the full signature or 10 percent of it, depending or whether |
groups |
Optional vector indicating the group ID of the samples |
scale. |
Logical, whether the data should be scaled |
two.tails |
Logical, whether a two tails, instead of 1 tail test should be performed |
ws |
Number indicating the exponent for the weighting the signatures, the default of 0 is uniform weighting, 1 is weighting by SD |
Object of class signatureDistance as a matrix of normalized enrichment scores
data(bcellViper, package="bcellViper") dd <- signatureDistance(exprs(dset)) dd[1:5, 1:5] scale(dd)[1:5, 1:5] as.matrix(as.dist(dd))[1:5, 1:5]data(bcellViper, package="bcellViper") dd <- signatureDistance(exprs(dset)) dd[1:5, 1:5] scale(dd)[1:5, 1:5] as.matrix(as.dist(dd))[1:5, 1:5]
This class contains the results generated by signatureDistance function.
Matrix of class numeric containing the similarity scores
This function transforms a numeric vector using a sigmoid function
sigT(x, slope = 20, inflection = 0.5)sigT(x, slope = 20, inflection = 0.5)
x |
Numeric vector |
slope |
Number indicating the slope at the inflection point |
inflection |
Number indicating the inflection point |
Numeric vector
This function generates a table of msviper results
## S3 method for class 'msviper' summary(object, mrs = 10, ...)## S3 method for class 'msviper' summary(object, mrs = 10, ...)
object |
msviper object |
mrs |
Either number of top MRs to report or vector containing the genes to display |
... |
Given for compatibility with the summary generic function |
Data.frame with results
This function performs sample permutation and t-test to generate a null model
ttestNull(x, ...) ## S4 method for signature 'matrix' ttestNull(x, y, per = 1000, repos = TRUE, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'ExpressionSet' ttestNull(x, pheno, group1, group2, per = 1000, repos = TRUE, seed = 1, verbose = TRUE)ttestNull(x, ...) ## S4 method for signature 'matrix' ttestNull(x, y, per = 1000, repos = TRUE, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'ExpressionSet' ttestNull(x, pheno, group1, group2, per = 1000, repos = TRUE, seed = 1, verbose = TRUE)
x |
ExpressionSet object or Matrix containing the test dataset |
... |
Additional parameters added to keep compatibility |
y |
Matrix containing the reference dataset |
per |
Integer indicating the number of permutations |
repos |
Logical, whether the permutations should be performed with reposition |
seed |
Integer indicating the seed for the permutations, 0 for disable it |
cores |
Integer indicating the number of cores to use (set to 1 in windows systems) |
verbose |
Logical, whether progression messages should be printed in the terminal |
pheno |
Character string indicating the phenotype data to use |
group1 |
Vector of character strings indicating the category from phenotype |
group2 |
Vector of character strings indicating the category from phenotype |
Matrix of z-scores with genes in rows and permutations in columns
data(bcellViper, package="bcellViper") d1 <- exprs(dset) dnull <- ttestNull(d1[, 1:10], d1[, 11:20], per=100) dim(dnull) plot(density(dnull)) data(bcellViper, package="bcellViper") dnull <- ttestNull(dset, "description", "CB", "CC", per=100) dim(dnull) plot(density(dnull))data(bcellViper, package="bcellViper") d1 <- exprs(dset) dnull <- ttestNull(d1[, 1:10], d1[, 11:20], per=100) dim(dnull) plot(density(dnull)) data(bcellViper, package="bcellViper") dnull <- ttestNull(dset, "description", "CB", "CC", per=100) dim(dnull) plot(density(dnull))
This function performs Virtual Inference of Protein-activity by Enriched Regulon analysis
viper(eset, regulon, dnull = NULL, pleiotropy = FALSE, nes = TRUE, method = c("none", "scale", "rank", "mad", "ttest"), bootstraps = 0, minsize = 25, adaptive.size = FALSE, eset.filter = TRUE, mvws = 1, pleiotropyArgs = list(regulators = 0.05, shadow = 0.05, targets = 10, penalty = 20, method = "adaptive"), cores = 1, verbose = TRUE)viper(eset, regulon, dnull = NULL, pleiotropy = FALSE, nes = TRUE, method = c("none", "scale", "rank", "mad", "ttest"), bootstraps = 0, minsize = 25, adaptive.size = FALSE, eset.filter = TRUE, mvws = 1, pleiotropyArgs = list(regulators = 0.05, shadow = 0.05, targets = 10, penalty = 20, method = "adaptive"), cores = 1, verbose = TRUE)
eset |
ExpressionSet object or Numeric matrix containing the expression data or gene expression signatures, with samples in columns and genes in rows |
regulon |
Object of class regulon or list of objects of class regulon for metaVIPER analysis |
dnull |
Numeric matrix for the null model, usually generated by |
pleiotropy |
Logical, whether correction for pleiotropic regulation should be performed |
nes |
Logical, whether the enrichment score reported should be normalized |
method |
Character string indicating the method for computing the single samples signature, either scale, rank, mad, ttest or none |
bootstraps |
Integer indicating the number of bootstraps iterations to perform. Only the scale method is implemented with bootstraps. |
minsize |
Integer indicating the minimum number of targets allowed per regulon |
adaptive.size |
Logical, whether the weighting scores should be taken into account for computing the regulon size |
eset.filter |
Logical, whether the dataset should be limited only to the genes represented in the interactome #' @param mvws Number or vector indicating either the exponent score for the metaViper weights, or the inflection point and trend for the sigmoid function describing the weights in metaViper |
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 method for computing the pleiotropy, 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 |
A matrix of inferred activity for each regulator gene in the network across all samples
data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- viper(d1, regulon) dim(d1) d1[1:5, 1:5] regulon dim(res) res[1:5, 1:5]data(bcellViper, package="bcellViper") d1 <- exprs(dset) res <- viper(d1, regulon) dim(d1) d1[1:5, 1:5] regulon dim(res) res[1:5, 1:5]
This function computes residual post-translational activity
viperRPT(vipermat, expmat, weights = matrix(1, nrow(vipermat), ncol(vipermat), dimnames = list(rownames(vipermat), colnames(vipermat))), method = c("spline", "lineal", "rank"), robust = FALSE, cores = 1)viperRPT(vipermat, expmat, weights = matrix(1, nrow(vipermat), ncol(vipermat), dimnames = list(rownames(vipermat), colnames(vipermat))), method = c("spline", "lineal", "rank"), robust = FALSE, cores = 1)
vipermat |
Numeric matrix containing the viper protein activity inferences |
expmat |
Numeric matrix or expressionSet containing the expression data |
weights |
List of numeric matrix of sample weights |
method |
Character string indicating the method to use, either rank, lineal or spline |
robust |
Logical, whether the contribution of outliers is down-weighted by using a gaussian kernel estimate for the join probability density |
cores |
Integer indicating the number of cores to use |
Matrix of RPT-activity values
data(bcellViper, package="bcellViper") vipermat <- viper(dset, regulon) rpt <- viperRPT(vipermat, dset) rpt[1:5, 1:5]data(bcellViper, package="bcellViper") vipermat <- viper(dset, regulon) rpt <- viperRPT(vipermat, dset) rpt[1:5, 1:5]
This function generates a viperSignature object from a test dataset based on a set of samples to use as reference
viperSignature(eset, ...) ## S4 method for signature 'ExpressionSet' viperSignature(eset, pheno, refgroup, method = c("zscore", "ttest", "mean"), per = 100, bootstrap = TRUE, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'matrix' viperSignature(eset, ref, method = c("zscore", "ttest", "mean"), per = 100, bootstrap = TRUE, seed = 1, cores = 1, verbose = TRUE)viperSignature(eset, ...) ## S4 method for signature 'ExpressionSet' viperSignature(eset, pheno, refgroup, method = c("zscore", "ttest", "mean"), per = 100, bootstrap = TRUE, seed = 1, cores = 1, verbose = TRUE) ## S4 method for signature 'matrix' viperSignature(eset, ref, method = c("zscore", "ttest", "mean"), per = 100, bootstrap = TRUE, seed = 1, cores = 1, verbose = TRUE)
eset |
ExpressionSet object or numeric matrix containing the test dataset, with genes in rows and samples in columns |
... |
Additional parameters added to keep compatibility |
pheno |
Character string indicating the phenotype data to use |
refgroup |
Vector of character string indicatig the category of |
method |
Character string indicating how to compute the signature and null model, either ttest, zscore or mean |
per |
Integer indicating the number of sample permutations |
bootstrap |
Logical, whether null model should be estimated with bootstrap. In this case, only reference samples are used. |
seed |
Integer indicating the seed for the random sample generation. The system default is used when set to zero |
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 |
ref |
Numeric matrix containing the reference samples (columns) and genes in rows |
viperSignature S3 object containing the signature and null model
data(bcellViper, package="bcellViper") ss <- viperSignature(dset, "description", c("N", "CB", "CC"), per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations res <- viper(ss, regulon) dim(exprs(dset)) exprs(dset)[1:5, 1:5] regulon dim(res) exprs(res)[1:5, 1:5] data(bcellViper, package="bcellViper") d1 <- exprs(dset) pos <- pData(dset)[["description"]] %in% c("N", "CB", "CC") ss <- viperSignature(d1[, !pos], d1[, pos], per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations res <- viper(ss, regulon) dim(d1) d1[1:5, 1:5] regulon dim(res) res[1:5, 1:5]data(bcellViper, package="bcellViper") ss <- viperSignature(dset, "description", c("N", "CB", "CC"), per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations res <- viper(ss, regulon) dim(exprs(dset)) exprs(dset)[1:5, 1:5] regulon dim(res) exprs(res)[1:5, 1:5] data(bcellViper, package="bcellViper") d1 <- exprs(dset) pos <- pData(dset)[["description"]] %in% c("N", "CB", "CC") ss <- viperSignature(d1[, !pos], d1[, pos], per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations res <- viper(ss, regulon) dim(d1) d1[1:5, 1:5] regulon dim(res) res[1:5, 1:5]
This class contains the results produced by the viperSignature function
signature:Matrix of class numeric with genes in rows and samples in columns containing the gene expression signatures
nullmodel:Matrix of class numeric with genes in rows and permutations in columns ontaining the sample-permutation based signatures to be used as NULL model
If ws is a single number, weighting is performed using an exponential function. If ws is a 2 numbers vector, weighting is performed with a symmetric sigmoid function using the first element as inflection point and the second as trend.
viperSimilarity(x, nn = NULL, ws = c(4, 2), method = c("two.sided", "greater", "less"))viperSimilarity(x, nn = NULL, ws = c(4, 2), method = c("two.sided", "greater", "less"))
x |
Numeric matrix containing the VIPER results with samples in columns and regulators in rows |
nn |
Optional number of top regulators to consider for computing the similarity |
ws |
Number indicating the weighting exponent for the signature, or vector of 2 numbers indicating the inflection point and the value corresponding to a weighting score of .1 for a sigmoid transformation, only used if |
method |
Character string indicating whether the most active (greater), less active (less) or both tails (two.sided) of the signature should be used for computing the similarity |
This function computes the similarity between VIPER signatures
signatureDistance object
data(bcellViper, package="bcellViper") dd <- viperSimilarity(exprs(dset)) dd[1:5, 1:5] scale(dd)[1:5, 1:5] as.matrix(as.dist(dd))[1:5, 1:5]data(bcellViper, package="bcellViper") dd <- viperSimilarity(exprs(dset)) dd[1:5, 1:5] scale(dd)[1:5, 1:5] as.matrix(as.dist(dd))[1:5, 1:5]