Package 'SUITOR'

Title: Selecting the number of mutational signatures through cross-validation
Description: An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.
Authors: DongHyuk Lee [aut], Bin Zhu [aut], Bill Wheeler [cre]
Maintainer: Bill Wheeler <[email protected]>
License: GPL-2
Version: 1.9.0
Built: 2024-10-31 05:38:11 UTC
Source: https://github.com/bioc/SUITOR

Help Index

Number of mutational signatures

Description

To select the number of mutational signatures through cross-validation.

Details

SUITOR (Selecting the nUmber of mutatIonal signaTures thrOugh cRoss-validation), an unsupervised cross-validation method that requires little assumptions and no numerical approximations to select the optimal number of signatures without overfitting the data. The full dataset of mutation counts is split into a training set and a validation set; for a given number of signatures, these signatures are estimated in the training set and then they are used to predict the mutations in the validation set. Multiple candidate numbers of signatures are considered; and the number of signatures which predicts most closely the mutations in the validation set is selected.

The two main functions in this package are suitor and suitorExtractWH.

Author(s)

Donghyuk Lee <[email protected]> and Bin Zhu <[email protected]>

References

Lee, D., Wang, D., Yang, X., Shi, J., Landi, M., Zhu, B. (2021) SUITOR: selecting the number of mutational signatures through cross-validation. bioRxiv, doi: https://doi.org/10.1101/2021.07.28.454269.

Compute summary results

Description

Compute summary results and the optimal rank from the matrix containing all results.

Usage

getSummary(obj, NC, NR=96)

Arguments

obj

Matrix containing all results in the return list from suitor.
NC

The number of columns in data when suitor was called.
NR

The number of rows in data when suitor was called. The default is 96.

Details

The input matrix obj must have column 1 as the rank, column 2 as the value of k in 1:k.fold, column 4 as the training errors, and column 5 as the testing errors.

Value

A list containing the objects:

  • rank: The optimal rank

  • all.results: Matrix containing training and testing errors for all values of seeds, ranks, folds. NA values appear for runs in which the EM algorithm did not converge.

  • summary: Data frame of summarized results for each possible rank created from all.results. The MSErr column is defined as sqrt({fold1 + ... +foldK}/{nrow(data)*ncol(data)})

Author(s)

Donghyuk Lee <[email protected]> and Bin Zhu <[email protected]>

See Also

plotErrors

Examples

data(SimData, package="SUITOR")
    data(results, package="SUITOR")
    ret <- getSummary(results$all.results, ncol(SimData))
    ret$summary
    ret$rank

Example data for plotting

Description

A data frame with columns Rank, Type, and MSErr

See Also

suitor

Examples

data(plotData, package="SUITOR")

    plotData

Plot train and test errors

Description

Plot train and test errors

Usage

plotErrors(x)

Arguments

x

Data frame of summary results in the return list from suitor or from getSummary, or a data frame with columns Rank, Type, and MSErr.

Details

The optimal rank is the minimum at which the test error is attained, and appears as a red dot on the graph.

Value

NULL

Author(s)

Donghyuk Lee <[email protected]> and Bin Zhu <[email protected]>

Examples

data(plotData, package="SUITOR")
    plotErrors(plotData)

suitor return object

Description

An object returned from the suitor function for examples

See Also

suitor

Examples

data(results, package="SUITOR")

    results

Data for examples

Description

Example input data and results

Details

Contains an example input data object of size 96 by 300. It is generated by rpois with mean WH where W (96 by 8) is profile of 8 signatures (SBS 4, 6, 7a, 9, 17b, 22, 26, 39) obtained from https://cancer.sanger.ac.uk/cosmic/signatures/SBS and H (8 by 300) is rounded integer generated from a uniform distribution between 0 and 100 with some randomly selected cells being set to zero.

See Also

suitor

Examples

data(SimData, package="SUITOR")

    # Display a subset of data objects
    SimData[1:5, 1:5]

suitor

Description

Selecting the number of mutational signatures through cross-validation

Usage

suitor(data, op=NULL)

Arguments

data

Data frame or matrix containing mutational signatures. This object must contain non-negative values
op

List of options (see details). The default is NULL.

Details

The algorithm finds the optimal rank by applying k-fold cross validation.

Options list op:

Name Description Default Value
em.eps EM algorithm stopping tolerance 1e-5
get.summary 0 or 1 to create summary results 1
k.fold Number of folds 10
max.iter Maximum number of iterations in EM algorithm 2000
max.rank Maximum rank 10
min.rank Minimum rank 1
min.value Minimum value of matrix before factorizing 1e-4
BPPARAM See BiocParallelParam NULL
n.starts Number of starting points 30
plot 0 or 1 to produce an error plot 1
print 0 or 1 to print info 1
kfold.vec Vector of values in 1:k.fold when running on a cluster NULL

Parallel computing
The BiocParallel package is used for parallel computing. If BPPARAM = NULL, then BPPARAM will be set to SerialParam.

Utilizing a cluster
When running on a cluster, the option get.summary should be set to 0. For fastest running jobs, set the options min.rank = max.rank, kfold.vec to a single integer in 1:k.fold, and n.starts to 1.

Value

A list containing the objects:

  • rank: The optimal rank

  • all.results: Matrix containing training and testing errors for all values of seeds, ranks, folds.

  • summary: Data frame of summarized results for each possible rank created from all.results. The MSErr column is defined as sqrt({fold1 + ... +foldK}/{nrow(data)*ncol(data)})

Author(s)

Donghyuk Lee <[email protected]> and Bin Zhu <[email protected]>

See Also

getSummary, plotErrors

Examples

data(SimData, package="SUITOR")

    # Using the default options will take several minutes to run
    ret <- suitor(SimData)

suitorExtractWH

Description

Extract the matrix of activities (exposures) and matrix of signatures

Usage

suitorExtractWH(data, rank, op=NULL)

Arguments

data

Data frame or matrix containing mutational signatures. This object must contain non-negative values
rank

Integer > 0
op

List of options (see details). The default is NULL.

Details

Options list op:

Name Description Default Value
min.value Minimum value of matrix before factorizing 1e-4
BPPARAM See BiocParallelParam NULL
n.starts Number of starting points 30
print 0 or 1 to print info 1

Parallel computing
The BiocParallel package is used for parallel computing. If BPPARAM = NULL, then BPPARAM will be set to SerialParam.

Value

A list containing the objects:

  • H: Matrix of activities (exposures)

  • W: Matrix of signatures

Author(s)

Donghyuk Lee <[email protected]> and Bin Zhu <[email protected]>

See Also

suitor

Examples

data(SimData, package="SUITOR")

    suitorExtractWH(SimData, 2)