Convert Signatures between different Genomic Distribution of Components

Source: R/sig_convert.R

Converts signatures between two representations relative to different sets of mutational opportunities. Currently, only SBS signature is supported.

sig_convert(sig, from = "human-genome", to = "human-exome")

Arguments

sig

a Signature object obtained either from sig_extract or sig_auto_extract, or just a raw signature matrix/data.frame with row representing components (motifs) and column representing signatures.

from

either one of "human-genome" and "human-exome" or an opportunity matrix (repeated n columns with each row represents the total number of mutations for a component, n is the number of signature).

to

same as from.

Value

a matrix.

Details

The default opportunity matrix for "human-genome" and "human-exome" comes from COSMIC signature database v2 and v3.

References

convert_signatures function from sigfit package.

Examples

# Load SBS signature
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
# Exome-relative to Genome-relative
sig_converted <- sig_convert(sig2,
  from = "human-exome",
  to = "human-genome"
)
sig_converted
#>                  Sig1          Sig2          Sig3
#> A[C>A]A  0.000000e+00  1.283652e-02 2.354578e-204
#> A[C>A]C  0.000000e+00  1.866572e-02  0.000000e+00
#> A[C>A]G  0.000000e+00  1.618700e-03  0.000000e+00
#> A[C>A]T  0.000000e+00  7.572233e-03  0.000000e+00
#> C[C>A]A  0.000000e+00  1.209076e-02  0.000000e+00
#> C[C>A]C  0.000000e+00  7.032249e-03 1.170400e-133
#> C[C>A]G  0.000000e+00  3.839313e-03 1.165310e-269
#> C[C>A]T  0.000000e+00  1.166974e-02  0.000000e+00
#> G[C>A]A  0.000000e+00  1.025669e-02  4.089543e-15
#> G[C>A]C 2.975389e-296  4.002311e-03  0.000000e+00
#> G[C>A]G  4.796114e-02 4.527374e-117  0.000000e+00
#> G[C>A]T  0.000000e+00  5.994876e-03 1.669814e-131
#> T[C>A]A  0.000000e+00  3.324941e-96  7.673114e-02
#> T[C>A]C  0.000000e+00  1.467589e-02 9.720402e-229
#> T[C>A]G  0.000000e+00  3.199454e-03  0.000000e+00
#> T[C>A]T  0.000000e+00  2.338506e-02  0.000000e+00
#> A[C>G]A  0.000000e+00  1.198076e-02 1.210238e-153
#> A[C>G]C  0.000000e+00  3.999796e-03  0.000000e+00
#> A[C>G]G  9.976549e-02  7.184837e-58  0.000000e+00
#> A[C>G]T  0.000000e+00  7.572233e-03 9.731662e-108
#> C[C>G]A  0.000000e+00  8.732217e-03  1.472610e-34
#> C[C>G]C  0.000000e+00  1.875266e-03  0.000000e+00
#> C[C>G]G  0.000000e+00  4.429976e-03  1.144811e-70
#> C[C>G]T  1.398527e-01  1.003533e-19  0.000000e+00
#> G[C>G]A 1.227107e-293  7.521572e-03 2.969058e-285
#> G[C>G]C  0.000000e+00  3.001734e-03 2.665595e-168
#> G[C>G]G  0.000000e+00  2.178881e-03  0.000000e+00
#> G[C>G]T  0.000000e+00  3.996584e-03  0.000000e+00
#> T[C>G]A  0.000000e+00  4.493267e-03 2.338585e-311
#> T[C>G]C  0.000000e+00  5.336688e-03 1.100445e-248
#> T[C>G]G  0.000000e+00  5.027714e-03 2.505791e-283
#> T[C>G]T  0.000000e+00  8.094828e-03  4.211703e-12
#> A[C>T]A  0.000000e+00  4.278842e-02 6.186711e-285
#> A[C>T]C  0.000000e+00  3.266500e-02 4.009287e-180
#> A[C>T]G  0.000000e+00  8.943317e-02 1.936180e-271
#> A[C>T]T  0.000000e+00  2.366323e-02  0.000000e+00
#> C[C>T]A  0.000000e+00  2.552494e-02  0.000000e+00
#> C[C>T]C  0.000000e+00  1.406450e-02 1.334078e-226
#> C[C>T]G  0.000000e+00  5.463637e-02 9.737288e-158
#> C[C>T]T  0.000000e+00  3.695418e-02 4.246509e-172
#> G[C>T]A  0.000000e+00 1.550033e-134  1.379990e-01
#> G[C>T]C  0.000000e+00  2.401387e-02 9.655208e-197
#> G[C>T]G  0.000000e+00  5.665090e-02 1.322415e-193
#> G[C>T]T  0.000000e+00  3.197267e-02 1.483309e-124
#> T[C>T]A  0.000000e+00  3.504749e-02 1.602583e-125
#> T[C>T]C  0.000000e+00  2.868470e-02 2.192251e-133
#> T[C>T]G  0.000000e+00  5.607061e-45  3.725237e-01
#> T[C>T]T  0.000000e+00  2.248563e-02 5.991874e-150
#> A[T>A]A  0.000000e+00 8.169022e-163 4.909543e-207
#> A[T>A]C  0.000000e+00  9.451235e-03 9.169290e-161
#> A[T>A]G  0.000000e+00 1.860257e-209  3.781700e-02
#> A[T>A]T  0.000000e+00  3.646724e-03  0.000000e+00
#> C[T>A]A  0.000000e+00  9.626354e-63 1.877035e-152
#> C[T>A]C  0.000000e+00  4.098575e-03  8.954807e-03
#> C[T>A]G  0.000000e+00  7.584736e-03  1.779246e-46
#> C[T>A]T  0.000000e+00  4.886651e-03  0.000000e+00
#> G[T>A]A  0.000000e+00 1.923466e-257  1.645056e-02
#> G[T>A]C  0.000000e+00  5.990275e-03 2.816093e-138
#> G[T>A]G  0.000000e+00  2.491146e-03 5.966918e-137
#> G[T>A]T  1.780073e-01 1.470587e-107  0.000000e+00
#> T[T>A]A  0.000000e+00  0.000000e+00  1.576605e-78
#> T[T>A]C  0.000000e+00 3.652510e-193  3.025830e-02
#> T[T>A]G  0.000000e+00  0.000000e+00  3.102984e-02
#> T[T>A]T  0.000000e+00  5.570191e-03 2.661350e-186
#> A[T>C]A  0.000000e+00  3.673499e-02 2.037390e-236
#> A[T>C]C  0.000000e+00  4.875997e-80  8.069896e-02
#> A[T>C]G  0.000000e+00  2.533400e-02 4.653276e-300
#> A[T>C]T  0.000000e+00  3.403610e-02 1.137147e-235
#> C[T>C]A  0.000000e+00  7.619558e-03  1.273356e-94
#> C[T>C]C  0.000000e+00  1.116095e-02 1.501723e-122
#> C[T>C]G  0.000000e+00  9.506418e-50  9.321794e-02
#> C[T>C]T  0.000000e+00  1.172796e-02  1.679251e-87
#> G[T>C]A  0.000000e+00  4.585040e-03  5.536247e-03
#> G[T>C]C  0.000000e+00 5.073564e-255  4.133148e-02
#> G[T>C]G  0.000000e+00  6.850650e-03  0.000000e+00
#> G[T>C]T  3.036787e-50  1.058999e-02 7.624782e-161
#> T[T>C]A  0.000000e+00 1.774320e-183  1.917769e-02
#> T[T>C]C 3.471970e-224  7.796288e-03  0.000000e+00
#> T[T>C]G  0.000000e+00  9.993850e-03  0.000000e+00
#> T[T>C]T  0.000000e+00  2.116673e-02 4.729625e-249
#> A[T>G]A  0.000000e+00  6.559820e-03  0.000000e+00
#> A[T>G]C  0.000000e+00 8.576821e-159  1.467254e-02
#> A[T>G]G  0.000000e+00  1.544237e-03  3.140069e-03
#> A[T>G]T  0.000000e+00  3.646724e-03  0.000000e+00
#> C[T>G]A  0.000000e+00  1.088508e-03  0.000000e+00
#> C[T>G]C  0.000000e+00  5.252213e-03 5.352907e-111
#> C[T>G]G  0.000000e+00  6.320613e-03  0.000000e+00
#> C[T>G]T  1.505897e-01  2.544085e-94 2.345935e-218
#> G[T>G]A  9.796461e-02  2.199487e-93 1.446688e-154
#> G[T>G]C  0.000000e+00  1.996758e-03  0.000000e+00
#> G[T>G]G  0.000000e+00  3.736718e-03  0.000000e+00
#> G[T>G]T  0.000000e+00  3.701349e-72  1.494581e-02
#> T[T>G]A  1.142049e-01 5.198170e-158  0.000000e+00
#> T[T>G]C  0.000000e+00  4.872680e-03  0.000000e+00
#> T[T>G]G  0.000000e+00  1.798724e-19  1.551492e-02
#> T[T>G]T  1.716541e-01  1.775134e-54  0.000000e+00

# \donttest{
show_sig_profile(sig2, style = "cosmic")

show_sig_profile(sig_converted, style = "cosmic")

# }