readShiraishiSignatures: Read a set of Shiraishi signatures.

In decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

Description

'readShiraishiSignatures()' reads one or more Shiraishi-type signatures from flat files (one file per signature). The signatures must be specified as matrices without headers and row names (see details below).

Usage

readShiraishiSignatures(files)

Arguments

files

(Mandatory) Can be a single file name, a vector of file names, or a list of file names.

Details

Format (see Shiraishi et al. PLoS Genetics 11(12):e1005657, 2015):

First line: Frequencies of the base changes C>A, C>G, C>T, T>A, T>C, and T>G

Following 2k lines (for k up- and downstream flanking bases): Frequencies of the bases A, C, G, and T, followed by two 0 values

Final line (only if transcription direction is considered): Frequencies of occurrences on the transcription strand, and on the opposite strand, followed by four 0 values.

Example:

1.8874e-14	0.10974	0.045918	0.11308	0.07429	0.65697
3.8079e-01	0.12215	0.191456	0.30561	0.00000	0.00000
1.5311e-01	0.34214	0.179774	0.32497	0.00000	0.00000
1.2378e-01	0.10243	0.163461	0.61032	0.00000	0.00000
3.4891e-01	0.15346	0.156687	0.34094	0.00000	0.00000
5.6435e-01	0.43565	0.000000	0.00000	0.00000	0.00000

Value

A list of Shiraishi signatures that can be used for decomposeTumorGenomes.

Author(s)

Rosario M. Piro, Politecnico di Milano
Sandra Krueger, Freie Universitaet Berlin
Maintainer: Rosario M. Piro
E-Mail: <[e-mail]> or <[e-mail]>

References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152.

See Also

decompTumor2Sig
readAlexandrovSignatures
getSignaturesFromEstParam

Examples

### read four Shiraishi signatures for breast cancer genomes from 
### Nik-Zainal et al (PMID: 22608084) from flat files
sigfiles <- system.file("extdata",
         paste0("Nik-Zainal_PMID_22608084-pmsignature-sig",1:4,".tsv"),
         package="decompTumor2Sig")

signatures <- readShiraishiSignatures(sigfiles)

decompTumor2Sig documentation built on Nov. 8, 2020, 8:23 p.m.