Description Usage Arguments Details Value See Also Examples
View source: R/extractSignatures.R
Decompose a matrix of 96 substitution classes into n
signatures.
1 2 3 4 5 6 7 | extractSignatures(
mat,
n = NULL,
plotBestFitRes = FALSE,
parallel = 4,
pConstant = NULL
)
|
mat |
Input matrix of diemnsion nx96 generated by |
n |
decompose matrix into n signatures. Default NULL. Tries to predict best value for |
plotBestFitRes |
plots consensus heatmap for range of values tried. Default FALSE |
parallel |
Default 4. Number of cores to use. |
pConstant |
A small positive value to add to the matrix. Use it ONLY if the functions throws an |
This function decomposes a non-negative matrix into n signatures.
a list with decomposed scaled signatures, signature contributions in each sample and NMF object.
trinucleotideMatrix
plotSignatures
compareSignatures
1 2 3 4 5 6 7 8 9 | ## Not run:
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
laml.tnm <- trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19', prefix = 'chr',
add = TRUE, useSyn = TRUE)
library("NMF")
laml.sign <- extractSignatures(mat = laml.tnm, plotBestFitRes = FALSE, n = 2, pConstant = 0.01)
## End(Not run)
|
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