getSignaturesFromEstParam {decompTumor2Sig} | R Documentation |
EstimatedParameters
object.'getSignaturesFromEstParam()' takes an EstimatedParameters
object
(signatures data) as computed by the 'pmsignature
' package (by
pmsignature::getPMSignature
; version 0.3.0) and extracts the
signature information. The signatures can then be passed to
decomposeTumorGenomes
.
getSignaturesFromEstParam(Param)
Param |
(Mandatory) A |
A list of Shiraishi signatures, one object per signature. Please
see readShiraishiSignatures
or the decompTumor2Sig
vignette
for more information on the format of Shiraishi signatures.
Rosario M. Piro and Sandra Krueger
Freie Universitaet Berlin
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or
<r.piro@fu-berlin.de>
http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2018) decompTumor2Sig: Identification of mutational
signatures active in individual tumors. BMC Bioinformatics (accepted for
publication).
Krueger, Piro (2017) Identification of Mutational Signatures Active in
Individual Tumors. NETTAB 2017 - Methods, Tools & Platforms for
Personalized Medicine in the Big Data Era, October 16-18, 2017, Palermo,
Italy. PeerJ Preprints 5:e3257v1, 2017.
decompTumor2Sig
readShiraishiSignatures
### load signatures for breast cancer genomes from ### Nik-Zainal et al (PMID: 22608084) in the format produced by ### pmsignature (PMID: 26630308) pmsigdata <- system.file("extdata", "Nik-Zainal_PMID_22608084-pmsignature-Param.Rdata", package="decompTumor2Sig") load(pmsigdata) ### extract the signatures from the pmsignature Param object signatures <- getSignaturesFromEstParam(Param)