table2df {mutSignatures}

Table Mutation Types by Sample.

Description

Prepare a molten data.frame starting from a mutation count matrix. Mutation types (rows) are countes for each sample (cols). The results are returned in a 3-column data.frame.

Usage

table2df(dataMatrix, rowLab = "sample", colLab = "feature", valueLab = "count")

Arguments

dataMatrix

a numeric matrix including mutation counts

rowLab

string, name for the column that will be storing row IDs, typically sample IDs

colLab

string, name for the column that will be storing column IDs, typically sample IDs

valueLab

string, name for the column that will be storing mutation count values

Details

This function is part of the user-interface set of tools included in mutSignatures. This is an exported function.

Value

data.frame storing mutation counts by sample

Author(s)

Damiano Fantini, [e-mail]

References

More information and examples about mutational signature analysis can be found here:

1. More info and examples about the mutSignatures R library: https://www.data-pulse.com/dev_site/mutsignatures/

2. Sci Rep paper, introducing mutS: https://www.nature.com/articles/s41598-020-75062-0/

3. Oncogene paper, Mutational Signatures Operative in Bladder Cancer: https://www.nature.com/articles/s41388-017-0099-6

Examples

A <- cbind(`A>G`=c(5,10),`A>T`=c(3,20),`A>C`=c(15,0))
rownames(A) = c("Smpl1", "Smpl2")
mutSignatures::table2df(A)