Estimate tumor purity, ploidy, and absolute copy number from a copy number segmentation.
Publication: Absolute quantification of somatic DNA alterations in human cancer (Carter et al. 2012).
This page on the GenePattern website contains some helpful information as well.
ABSOLUTE receives the following inputs:
- Segmented, smoothed (relative) copy number profiles
- I.e., from HapASeg or AllelicCapSeg
- Somatic point mutations with their allelic fractions
ABSOLUTE uses these as evidence to infer the following quantities:
- Tumor purity
- Tumor ploidy
- Absolute copy numbers for genome segments
The ABSOLUTE R script (ABSOLUTE_cli_start.R) outputs the following files:
*.ABSOLUTE_plot.pdf. Plots of ABSOLUTE candidate solutions*.PP-modes.data.RData. RData file containing candidate solutions
Once a candidate solution is chosen, the "extractor" script (ABSOLUTE_extract_cli_start.R) can produce the following outputs:
{sample_name}_ABS_MAF.txt{sample_name}.segtab.txt{sample_name}.ABSOLUTE.{analyst_id}.called.RData- RData file containing a list of candidate ABSOLUTE solutions
{sample_name}.{analyst_id}.ABSOLUTE.table.txt- Contains purities and ploidies. Analyst can edit this file with manual annotations in order to