Estimates tumor purity by fitting coverage and MAF segmentation data across a range of purity values, selecting the purity that best matches integer copy number models.
Usage
EstimatePurityCov(seg, gender)
Arguments
- seg
A data frame or tibble of segment data, with columns: Chromosome, Segment_Mean, MAF, MAF_gmm_G, MAF_Probes, MAF_gmm_weight, size, etc.
- gender
Gender male or femal.
Value
A list with elements:
- dis_df
Data frame of model fit statistics for each purity.
- Final_model
List with Final_mu and Final_rho (the selected purity).
- min_dis
Minimum distance to integer copy numbers.
- seg_call
Segment calls for the selected purity.
- Model_source
String, always "Coverage".
Details
This function fits models for a sequence of purity values, applies segment correction and calling, and selects the purity with the best fit to integer copy number.
