GSE129785_SU008_Tumor_Pre {scPloidy}

Basal cell carcinoma sample SU008_Tumor_Pre

Description

The dataset includes 788 nuclei obtained from basal cell carcinoma sample SU008_Tumor_Pre. Overlapping of single-nucleus ATAC-seq fragments was computed with the fragmentoverlapcount function.

Usage

data(GSE129785_SU008_Tumor_Pre)

SU008_Tumor_Pre_windowcovariates

rescnv

Format

SU008_Tumor_Pre_fragmentoverlap is a dataframe of fragmentoverlap.

SU008_Tumor_Pre_windowcovariates is a dataframe of windows and peaks.

rescnv is a list containing the output of cnv function.

Source

GEO, GSE129785

References

Satpathy et al. (2019) Nature Biotechnology 37:925 doi:10.1038/s41587-019-0206-z

Examples

## Not run: 
data(GSE129785_SU008_Tumor_Pre)
levels = c(2, 4)
result = cnv(SU008_Tumor_Pre_fragmentoverlap,
             SU008_Tumor_Pre_windowcovariates,
             levels = levels,
             deltaBICthreshold = -600)

## End(Not run)