sig_get_similarity

signature 1, result of <a rd-options="" href="/link/sig_extract?package=sigminer&version=0.1.11" data-mini-rdoc="sigminer::sig_extract">sig_extract</a> function or
a <code>data.frame</code> which rows are features and columns are signatures
(colnames are necessary).

sig1

signature 2, result of <a rd-options="" href="/link/sig_extract?package=sigminer&version=0.1.11" data-mini-rdoc="sigminer::sig_extract">sig_extract</a> function or
a <code>data.frame</code> which rows are features and columns are signatures
(colnames are necessary).

sig2

could be "cos" (default, cosine similarity) or "cor" (correlation).

type

Obtain similarity for two signature matrix, their rows (features) must match.

Contains functions for identification of
copy number signatures (Geoffrey et al. (2018) <doi:10.1038/s41588-018-0179-8>) and
mutation signatures (Alexandrov et al. (2013) <doi:10.1038/nature12477>)
by non-negative matrix factorization, signature analysis and visualization.
It can be used to capture signatures of genomic variation, compare genotype or
phenotype features of different signatures and thus uncover the relationship
between the mechanism of genomic variation and phenotypes in cancer.

Shixiang Wang

sigminer

Capture Genomic Variation Signatures using Non-Negative Matrix
Factorization

Geoffrey Macintyre

Xue-Song Liu

sig_get_similarity function

signature 1, result of <a rd-options='' href='sig_extract'>sig_extract</a> function or
a <code>data.frame</code> which rows are features and columns are signatures
(colnames are necessary).

signature 2, result of <a rd-options='' href='sig_extract'>sig_extract</a> function or
a <code>data.frame</code> which rows are features and columns are signatures
(colnames are necessary).

sig_get_similarity: Get similarity between signatures

Description

Usage

Arguments

Value

See Also