readShiraishiSignatures {decompTumor2Sig} | R Documentation

## Read a set of Shiraishi signatures.

### 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: <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

    ### 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)

[Package decompTumor2Sig version 2.10.0 Index]