isa: Iterative Signature Algorithm

Description

Run ISA with the default parameters

Usage

# S4 method for matrix
isa(data, ...)

Value

A named list is returned with the following elements:

rows

The row components in the biclusters, a numeric matrix. Every column in it corresponds to a bicluster, if an element (the score of the row) is non-zero, that means that the row is included in the bicluster, otherwise it is not. Scores are between -1 and 1. If the scores of two rows have the same (nonzero) sign, that means that the two corresponding rows “behave” the same way. If they have opposite sign, that means that they behave the opposite way.

If the corresponding seed has not converged during the allowed number of iterations, then that column of rows contains NA values.

columns

The column components of the biclusters, in the same format as the rows.

If the corresponding seed has not converged during the allowed number of iterations, then that column of columns contains NA values.

seeddata

A data frame containing information about the biclusters. There is one row for each bicluster. The data frame has the following columns:

iterations: The number of iterations needed to converge to the bicluster.

oscillation

The oscillation period for oscillating biclusters. It is zero for non-oscillating ones.

thr.row

The row threshold that was used for find the bicluster.

thr.col

The column threshold that was used for finding the bicluster.

freq

The number of times the bicluster was found.

rob

The robustness score of the bicluster, see robustness for details.

rob.limit

The robustness limit that was used to filter the module. See isa.filter.robust for details.

rundata

A named list with information about the ISA runs. It has the following entries:

direction: Character vector of length two. Specifies which side(s) of the score distribution were kept in each ISA step. See the direction argument of isa.iterate for details.

convergence

Character scalar. The convergence criteria for the iteration. See the convergence argument of isa.iterate for details.

eps

Numeric scalar. The threshold for convergence, if the ‘eps’ convergence criteria was used.

cor.limit

Numeric scalar. The threshold for convergence, if the ‘cor’ convergence criteria was used.

corx

Numeric scalar, the shift in number of iterations, to check convergence. See the convergence argument of isa.iterate for details.

maxiter

Numeric scalar. The maximum number of iterations that were allowed for an input seed.

N

Numeric scalar. The total number of seeds that were used for all the thresholds.

prenormalize

Logical scalar. Whether the data was pre-normalized.

hasNA

Logical scalar. Whether the (normalized) data had NA or NaN values.

unique

Logical scalar. Whether the similar biclusters were merged by calling isa.unique.

oscillation

Logical scalar. Whether the algorithm looked for oscillating modules as well.

rob.perms

Numeric scalar, the number of permutations that were used to calculate the baseline robustness for filtering. See the perms argument of the isa.filter.robust function for details.

Arguments

data: The input. It must be a numeric matrix. It may contain NA and/or NaN values, but then the algorithm might be a bit slower, as R matrix multiplication might be slower for these matrices, depending on your platform.
...: Additional arguments, see details below.

Author

Gabor Csardi Gabor.Csardi@unil.ch

Details

Please read the isa2-package manual page for an introduction on ISA.

This function can be called as


    isa(data, thr.row=seq(1,3,by=0.5),
        thr.col=seq(1,3,by=0.5), no.seeds=100,
        direction=c("updown", "updown"))

where the arguments are:

data: The input. It must be a numeric matrix. It may contain NA and/or NaN values, but then the algorithm might be a bit slower, as R matrix multiplication might be slower for these matrices, depending on your platform.
thr.row: Numeric vector. The row threshold parameters for which the ISA will be run. We use all possible combinations of thr.row and thr.col.
thr.col: Numeric vector. The column threshold parameters for which the ISA will be run. We use all possible combinations of thr.row and thr.col.
no.seeds: Integer scalar, the number of seeds to use.
direction: Character vector of length two, one for the rows, one for the columns. It specifies whether we are interested in rows/columns that are higher (‘up’) than average, lower than average (‘down’), or both (‘updown’).

The isa function provides an easy to use interface to the ISA. It runs all steps of a typical ISA work flow with their default parameters.

This involves:

Normalizing the data by calling isa.normalize.
Generating random input seeds via generate.seeds.
Running ISA with all combinations of given row and column thresholds, (by default 1, 1.5, 2, 2.5, 3); by calling isa.iterate.
Merging similar modules, separately for each threshold combination, by calling isa.unique.
Filtering the modules separately for each threshold combination, by calling isa.filter.robust.
Putting all modules from the runs with different thresholds into a single object.
Merging similar modules, across all threshold combinations, if two modules are similar, then the larger one, the one with the milder thresholds is kept.

Please see the manual pages of these functions for the details or if you want to change their default parameters.

References

Bergmann S, Ihmels J, Barkai N: Iterative signature algorithm for the analysis of large-scale gene expression data Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Mar;67(3 Pt 1):031902. Epub 2003 Mar 11.

Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, Barkai N: Revealing modular organization in the yeast transcriptional network Nat Genet. 2002 Aug;31(4):370-7. Epub 2002 Jul 22

Ihmels J, Bergmann S, Barkai N: Defining transcription modules using large-scale gene expression data Bioinformatics 2004 Sep 1;20(13):1993-2003. Epub 2004 Mar 25.

Examples

Run this code

if (FALSE) {
## We generate some noisy in-silico data with modules and try to find
## them with the ISA. This might take one or two minutes.
data <- isa.in.silico(noise=0.1)
isa.result <- isa(data[[1]])

## Find the best bicluster for each block in the input
best <- apply(cor(isa.result$rows, data[[2]]), 2, which.max)

## Check correlation
sapply(seq_along(best),
       function(x) cor(isa.result$rows[,best[x]], data[[2]][,x]))

## The same for the columns
sapply(seq_along(best),
       function(x) cor(isa.result$columns[,best[x]], data[[3]][,x]))

## Plot the data and the modules found
if (interactive()) {
  layout(rbind(1:2,3:4))
  image(data[[1]], main="In-silico data")
  sapply(best, function(b) image(outer(isa.result$rows[,b],
                                       isa.result$columns[,b]),
                                 main=paste("Module", b)))  
}
}

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