snv_extractSignatures: Extract mutational signatures from trinucleotide context.
In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description Usage Arguments Details Value See Also Examples

Decompose a matrix of 96 substitution classes into n signatures.

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snv_extractSignatures(mat, n = NULL, nrun = 1, nTry = 6,
  nrun_Try = 10, plotBestFitRes = FALSE, parallel = NULL,
  pConstant = NULL)

`mat`	Input matrix of diemnsion nx96 generated by `trinucleotideMatrix`
`n`	decompose matrix into n signatures. Default NULL. Tries to predict best value for `n` by running NMF on a range of values and chooses based on cophenetic correlation coefficient.
`nrun`	number of runs to perform on user specified rank.
`nTry`	tries upto this number of signatures before choosing best `n`. Default 6.
`nrun_Try`	number of runs to perform when obtain a best-fit rank for NMF.
`plotBestFitRes`	plots consensus heatmap for range of values tried. Default FALSE
`parallel`	calls to .opt argument of `nmf`. e.g, 'P4' for using 4 cores. See note on `nmf` for MAC users.
`pConstant`	A small positive value to add to the matrix. Use it ONLY if the functions throws an `non-conformable arrays` error

This function decomposes a non-negative matrix into n signatures. Extracted signatures are compared against 30 experimentally validated signatures by calculating cosine similarity. See http://cancer.sanger.ac.uk/cosmic/signatures for details.

a list with decomposed scaled signatures, signature contributions in each sample and a cosine similarity table against validated signatures.

Other SNV analysis functions: snv_plotSignatures, snv_readprofile, snv_signatureEnrichment, snv_trinucleotideMatrix

## Not run: 
laml.tnm <- snv_trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19',
    prefix = 'chr', add = TRUE, useSyn = TRUE)
laml.sign <- snv_extractSignatures(mat = laml.tnm, plotBestFitRes = FALSE)

## End(Not run)