sigs_pcawg {YAPSA} | R Documentation |
PCAWG_SP_SBS_sigs_Artif_df
: Data frame of the signatures published
by Alexandrov et al. (Biorxiv 2013) which were decomposed with the
method SigProfiler. SNV signatures are labeled with SBS, single base
signature. There are 67 signatures which constitute the columns, 47 of
which were validated by a bayesian NFM mehtod, SignatureAnayzer. Validated
signatures are SBS1-SBS26,SBS28-SBS42 and SBS44. SBS7 is split up into
7 a/b/c and d. SBS10 ans SBS17 are both split up into a and b. Resulting in
a 47 validated sigantures. Please note, unlike the paper by Alexandrov et al.
(Biorxiv 2018) the data sets do not contain a SBS84 and SBS85 as not all
were availiablt to perfom supervised signature analysis. In total there are
96 different features and therefore 96 rows when dealing with a trinucleotide
context.PCAWG_SP_SBS_sigInd_Artif_df
: Meta-information for
PCAWG_SP_SBS_sigs_Artif_df
PCAWG_SP_SBS_sigs_Real_df
: Data frame of only the validated
signatures published by Alexandrov et al. (Biorxiv 2018), corresponding
to the column 1-26, 28-42 and 44 of the PCAWG_SP_SBS_sigs_Artif_df
data frame
PCAWG_SP_SBS_sigInd_Real_df
: Meta-information for
PCAWG_SP_SBS_sigs_Real_df
PCAWG_SP_ID_sigs_df
: Data frame with Indel signatures published by
Alexandrov et al. (Biorxiv 2018) which were decomposed with the method
SigProfiler. There are 17 Sigantures reported but as supervised signatures
are only valid for whole genome sequencing data analysis. In whole genome
sequencing data the Indel signature ID15 was not discribed and thus is not
part of this data set. In total 83 features are described. The categorization
consideres the size of the insertion and delition, the motif, and the
sequence context. Hereby the number of repetition or patial repetition of the
motif is determined.
PCAWG_SP_ID_sigInd_df
: Meta-information for
PCAWG_SP_ID_sigs_df
data(sigs_pcawg)
Lea Jopp-Saile huebschmann.daniel@googlemail.com
PCAWG_SNV
: https://www.synapse.org/#!Synapse:syn11738319
PCAWG_INDEL
: https://cancer.sanger.ac.uk/cosmic/ signatures/ID
Alexandrov et al. (Biorxiv 2018)