readShiraishiSignatures: Read a set of Shiraishi signatures.

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/readShiraishiSignatures.R

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

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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: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>

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

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### 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.