Overview

The goal of sigminer is to provide an uniform interface for genomic variation signature analysis and visualization. sigminer is originated from VSHunter package I wrote. I hate ugly structure and function names in VSHunter, thus reconstruct it using concise function names, S4 classes and S3 methods etc.. I will continue to add more features to uncover genomic variation signatures and their correlationship with phenotypes and genotypes.

sigminer is powered by NMF package and maftools package.

Installation

You can install the stable release of sigminer from CRAN with:

You can also install the development version of sigminer from Github with:

Usage

An example for how to extract mutational signatures are given as the following.

Load data as a MAF object

laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read_maf(maf = laml.maf)
#> reading maf..
#> silent variants: 475
#>         ID   N
#> 1: Samples 157
#> 2: 5'Flank   3
#> 3:     IGR   5
#> 4:  Intron   8
#> 5:     RNA  10
#> 6:  Silent 449
#> Summarizing..
#>                    ID          summary  Mean Median
#>  1:        NCBI_Build               37    NA     NA
#>  2:            Center genome.wustl.edu    NA     NA
#>  3:           Samples              193    NA     NA
#>  4:            nGenes             1241    NA     NA
#>  5:   Frame_Shift_Del               52 0.271      0
#>  6:   Frame_Shift_Ins               91 0.474      0
#>  7:      In_Frame_Del               10 0.052      0
#>  8:      In_Frame_Ins               42 0.219      0
#>  9: Missense_Mutation             1342 6.990      7
#> 10: Nonsense_Mutation              103 0.536      0
#> 11:       Splice_Site               92 0.479      0
#> 12:             total             1732 9.021      9
#> Gene Summary..
#>       Hugo_Symbol Frame_Shift_Del Frame_Shift_Ins In_Frame_Del
#>    1:        FLT3               0               0            1
#>    2:      DNMT3A               4               0            0
#>    3:        NPM1               0              33            0
#>    4:        IDH2               0               0            0
#>    5:        IDH1               0               0            0
#>   ---                                                         
#> 1237:      ZNF689               0               0            0
#> 1238:      ZNF75D               0               0            0
#> 1239:      ZNF827               1               0            0
#> 1240:       ZNF99               0               0            0
#> 1241:        ZPBP               0               0            0
#>       In_Frame_Ins Missense_Mutation Nonsense_Mutation Splice_Site total
#>    1:           33                15                 0           3    52
#>    2:            0                39                 5           6    54
#>    3:            0                 1                 0           0    34
#>    4:            0                20                 0           0    20
#>    5:            0                18                 0           0    18
#>   ---                                                                   
#> 1237:            0                 1                 0           0     1
#> 1238:            0                 1                 0           0     1
#> 1239:            0                 0                 0           0     1
#> 1240:            0                 1                 0           0     1
#> 1241:            0                 1                 0           0     1
#>       MutatedSamples AlteredSamples
#>    1:             52             52
#>    2:             48             48
#>    3:             33             33
#>    4:             20             20
#>    5:             18             18
#>   ---                              
#> 1237:              1              1
#> 1238:              1              1
#> 1239:              1              1
#> 1240:              1              1
#> 1241:              1              1
#> Checking clinical data..
#> NOTE: Missing clinical data! It is strongly recommended to provide clinical data associated with samples if available.
#> Done !

Citation

If you use sigminer in academic field, please cite:

Wang, Shixiang, et al. “APOBEC3B and APOBEC mutational signature as
    potential predictive markers for immunotherapy response in non-small
    cell lung cancer.” Oncogene (2018).

and

Gaujoux, Renaud, and Cathal Seoighe. "A Flexible R Package for 
    Nonnegative Matrix Factorization."" BMC Bioinformatics 11, no. 1 (December 2010).

Acknowledgments

The code for extracting copy number signatures was based in part on the source code from paper Copy number signatures and mutational processes in ovarian carcinoma, if you use this feature, please also cite:

Macintyre, Geoff, et al. "Copy number signatures and mutational
    processes in ovarian carcinoma." Nature genetics 50.9 (2018): 1262.

The code for extracting mutational signatures was based in part on the source code of the maftools package, if you use this feature, please also cite:

Mayakonda, Anand, et al. "Maftools: efficient and comprehensive analysis
    of somatic variants in cancer." Genome research 28.11 (2018): 1747-1756.

LICENSE

MIT © 2019 Shixiang Wang, Geoffrey Macintyre, Xue-Song Liu