inst/extdata/metadata_help.md

In rvalieris/signeR: Empirical Bayesian approach to mutational signature discovery

Metadata matrix

Clinical data is a tab-delimited text file with a matrix of available metadata (clinical and/or survival) for each sample. It must have a first column of sample IDs, named “SampleID”, whose entries match the row names of the SNV matrix. The number and title of the remaining columns are optional, however if survival data is included it must be organized in a column named time (in months) and another named status (which contains 1 for death events and 0 for censored samples). The table below shows an example of the clinical data matrix structure.

SampleID gender ajcc_pathologic_stage ethnicity race status time PD3851a male Stage I not hispanic or latino white 0 236 PD3890a male Stage II not hispanic or latino black or african american 1 199 PD3904a female Stage II NA NA 0 745 PD3905a female Stage IV NA white 1 299 PD3945a male Stage IV not hispanic or latino asian 0 799

Columns

The first column must contain the sample ID. Other columns may contain sample groupings or other features that you would like to co-analyze with exposure data.

Rows

Each row contains clinical information for one sample: its ID and all other data of interest.

Example file

21 breast cancer

rvalieris/signeR documentation built on April 20, 2024, 2:08 p.m.