mutSigData: Input Data and Examples for Running Mutational Signatures...

In mutSignatures: Decipher Mutational Signatures from Somatic Mutational Catalogs

Description

A series of objects, including collections of DNA mutations from 50 Bladder cancer samples, as well as mutational signatures extracted from the same samples. Mutation catalogs were obtained from a TCGA bladder cancer dataset (data available from the BROAD Institute). Original sample IDs were shuffled and then re-encoded. Data are available in different formats, and can be used as input for running mutational signature analyses.

Usage

data("mutSigData")

Format

A list with 6 elements. Each element is a different type of mutSignatures input/data:

inputA

data.frame with 10401 rows and 4 columns. DNA mutation data mimicking a TCGA dataset downloaded using TCGAretriever/cBio

inputB

data.frame with 13523 rows and 12 columns. DNA mutation data mimicking a TCGA MAF file

inputC

data.frame with 13523 rows and 11 columns. DNA mutation data mimicking a VCF file decorated with a SAMPLEID column

inputC.ctx

data.frame with 13523 rows and 11 columns. DNA mutation data mimicking a VCF file decorated with a SAMPLEID column

inputD

data.frame with 13487 rows and 56 columns. DNA mutation data mimicking a set of VCF files casted into a 2D matrix (samples as columns)

inputS

list including data for silhouette plot generation (used in the vignette)

blcaMUTS

data.frame with 96 rows and 50 columns. A table of DNA mutation counts (rows are mutation types; columns are samples)

blcaSIGS

data.frame with 96 rows and 8 columns. Set of 8 mutational signatures (rows are mutation types; columns are signatures)

.addON

list of add-on functions (executed only upon request, not evaluated; these may require manual installation of external libraries from Bioconductor or GitHUB)

Details

Examples and more information are available in the vignette, as well as at the following URL: https://www.data-pulse.com/dev_site/mutsignatures/

Source

BLCA data were downloaded from http://gdac.broadinstitute.org/ and then further processed, modified, and formatted.

Examples

data(mutSigData)
print(mutSigData$input.A[1:6,])

mutSignatures documentation built on Nov. 9, 2020, 9:06 a.m.