Source code for

"""Call copy number variants from segmented log2 ratios."""
import logging

import numpy as np
import pandas as pd

from . import segfilters

[docs]def do_call(cnarr, variants=None, method="threshold", ploidy=2, purity=None, is_reference_male=False, is_sample_female=False, filters=None, thresholds=(-1.1, -0.25, 0.2, 0.7)): if method not in ("threshold", "clonal", "none"): raise ValueError("Argument `method` must be one of: clonal, threshold") outarr = cnarr.copy() if filters: # Apply any filters that use segmetrics but not cn fields for filt in ('ci', 'sem'): if filt in filters:"Applying filter '%s'", filt) outarr = getattr(segfilters, filt)(outarr) filters.remove(filt) if variants: outarr["baf"] = variants.baf_by_ranges(outarr) if purity and purity < 1.0:"Rescaling sample with purity %g, ploidy %d", purity, ploidy) absolutes = absolute_clonal(outarr, ploidy, purity, is_reference_male, is_sample_female) # Recalculate sample log2 ratios after rescaling for purity outarr["log2"] = log2_ratios(outarr, absolutes, ploidy, is_reference_male) if variants: # Rescale b-allele frequencies for purity outarr["baf"] = rescale_baf(purity, outarr["baf"]) elif method == "clonal": # Estimate absolute copy numbers from the original log2 values"Calling copy number with clonal ploidy %d", ploidy) absolutes = absolute_pure(outarr, ploidy, is_reference_male) if method == "threshold": # Apply cutoffs to either original or rescaled log2 values tokens = ["%g => %d" % (thr, i) for i, thr in enumerate(thresholds)]"Calling copy number with thresholds: %s", ", ".join(tokens)) absolutes = absolute_threshold(outarr, ploidy, thresholds, is_reference_male) if method != 'none': outarr['cn'] = absolutes.round().astype('int') if 'baf' in outarr: # Calculate major and minor allelic copy numbers (s.t. cn1 >= cn2) upper_baf = ((outarr['baf'] - .5).abs() + .5).fillna(1.0).values outarr['cn1'] = ((absolutes * upper_baf).round() .clip(0, outarr['cn']) .astype('int')) outarr['cn2'] = outarr['cn'] - outarr['cn1'] is_null = (outarr['baf'].isnull() & (outarr['cn'] > 0)) outarr[is_null, 'cn1'] = np.nan outarr[is_null, 'cn2'] = np.nan if filters: # Apply the remaining cn-based filters for filt in filters: if not logging.warning("Resetting index") # DBG = logging.warning("Applying filter '%s'", filt) outarr = getattr(segfilters, filt)(outarr) outarr.sort_columns() return outarr
[docs]def log2_ratios(cnarr, absolutes, ploidy, is_reference_male, min_abs_val=1e-3, round_to_int=False): """Convert absolute copy numbers to log2 ratios. Optionally round copy numbers to integers. Account for reference sex & ploidy of sex chromosomes. """ # Round absolute copy numbers to integer values if round_to_int: absolutes = absolutes.round() # Avoid a logarithm domain error ratios = np.log2(np.maximum(absolutes / ploidy, min_abs_val)) # Adjust sex chromosomes to be relative to the reference if is_reference_male: ratios[(cnarr.chromosome == cnarr._chr_x_label).values] += 1.0 ratios[(cnarr.chromosome == cnarr._chr_y_label).values] += 1.0 return ratios
[docs]def absolute_threshold(cnarr, ploidy, thresholds, is_reference_male): """Call integer copy number using hard thresholds for each level. Integer values are assigned for log2 ratio values less than each given threshold value in sequence, counting up from zero. Above the last threshold value, integer copy numbers are called assuming full purity, diploidy, and rounding up. Default thresholds follow this heuristic for calling CNAs in a tumor sample: For single-copy gains and losses, assume 50% tumor cell clonality (including normal cell contamination). Then:: R> log2(2:6 / 4) -1.0 -0.4150375 0.0 0.3219281 0.5849625 Allowing for random noise of +/- 0.1, the cutoffs are:: DEL(0) < -1.1 LOSS(1) < -0.25 GAIN(3) >= +0.2 AMP(4) >= +0.7 For germline samples, better precision could be achieved with:: LOSS(1) < -0.4 GAIN(3) >= +0.3 """ absolutes = np.zeros(len(cnarr), dtype=np.float_) for idx, row in enumerate(cnarr): ref_copies = _reference_copies_pure(row.chromosome, ploidy, is_reference_male) if np.isnan(row.log2): # XXX fallback logging.warning("log2=nan found; replacing with neutral copy number %s", ref_copies) absolutes[idx] = ref_copies continue cnum = 0 for cnum, thresh in enumerate(thresholds): if row.log2 <= thresh: if ref_copies != ploidy: cnum = int(cnum * ref_copies / ploidy) break else: cnum = int(np.ceil(_log2_ratio_to_absolute_pure(row.log2, ref_copies))) absolutes[idx] = cnum return absolutes
[docs]def absolute_clonal(cnarr, ploidy, purity, is_reference_male, is_sample_female): """Calculate absolute copy number values from segment or bin log2 ratios.""" absolutes = np.zeros(len(cnarr), dtype=np.float_) for i, row in enumerate(cnarr): # TODO by_chromosome to reduce number of calls to this ref_copies, expect_copies = _reference_expect_copies( row.chromosome, ploidy, is_sample_female, is_reference_male) absolutes[i] = _log2_ratio_to_absolute( row.log2, ref_copies, expect_copies, purity) return absolutes
[docs]def absolute_pure(cnarr, ploidy, is_reference_male): """Calculate absolute copy number values from segment or bin log2 ratios.""" absolutes = np.zeros(len(cnarr), dtype=np.float_) for i, row in enumerate(cnarr): ref_copies = _reference_copies_pure(row.chromosome, ploidy, is_reference_male) absolutes[i] = _log2_ratio_to_absolute_pure(row.log2, ref_copies) return absolutes
[docs]def absolute_dataframe(cnarr, ploidy, purity, is_reference_male, is_sample_female): """Absolute, expected and reference copy number in a DataFrame.""" absolutes = np.zeros(len(cnarr), dtype=np.float_) reference_copies = expect_copies = np.zeros(len(cnarr), dtype=np.int_) for i, row in enumerate(cnarr): ref_copies, exp_copies = _reference_expect_copies( row.chromosome, ploidy, is_sample_female, is_reference_male) reference_copies[i] = ref_copies expect_copies[i] = exp_copies absolutes[i] = _log2_ratio_to_absolute( row.log2, ref_copies, exp_copies, purity) return pd.DataFrame({'absolute': absolutes, 'reference': reference_copies, 'expect': expect_copies})
[docs]def absolute_expect(cnarr, ploidy, is_sample_female): """Absolute integer number of expected copies in each bin. I.e. the given ploidy for autosomes, and XY or XX sex chromosome counts according to the sample's specified chromosomal sex. """ exp_copies = np.repeat(ploidy, len(cnarr)) is_y = (cnarr.chromosome == cnarr._chr_y_label).values if is_sample_female: exp_copies[is_y] = 0 else: is_x = (cnarr.chromosome == cnarr._chr_x_label).values exp_copies[is_x | is_y] = ploidy // 2 return exp_copies
[docs]def absolute_reference(cnarr, ploidy, is_reference_male): """Absolute integer number of reference copies in each bin. I.e. the given ploidy for autosomes, 1 or 2 X according to the reference sex, and always 1 copy of Y. """ ref_copies = np.repeat(ploidy, len(cnarr)) is_x = (cnarr.chromosome == cnarr._chr_x_label).values is_y = (cnarr.chromosome == cnarr._chr_y_label).values if is_reference_male: ref_copies[is_x] = ploidy // 2 ref_copies[is_y] = ploidy // 2 return ref_copies
def _reference_expect_copies(chrom, ploidy, is_sample_female, is_reference_male): """Determine the number copies of a chromosome expected and in reference. For sex chromosomes, these values may not be the same ploidy as the autosomes. The "reference" number is the chromosome's ploidy in the CNVkit reference, while "expect" is the chromosome's neutral ploidy in the given sample, based on the specified sex of each. E.g., given a female sample and a male reference, on chromosome X the "reference" value is 1 but "expect" is 2. Returns ------- tuple A pair of integers: number of copies in the reference, and expected in the sample. """ chrom = chrom.lower() if chrom in ["chrx", "x"]: ref_copies = (ploidy // 2 if is_reference_male else ploidy) exp_copies = (ploidy if is_sample_female else ploidy // 2) elif chrom in ["chry", "y"]: ref_copies = ploidy // 2 exp_copies = (0 if is_sample_female else ploidy // 2) else: ref_copies = exp_copies = ploidy return ref_copies, exp_copies def _reference_copies_pure(chrom, ploidy, is_reference_male): """Determine the reference number of chromosome copies (pure sample). Returns ------- int Number of copies in the reference. """ chrom = chrom.lower() if chrom in ["chry", "y"] or (is_reference_male and chrom in ["chrx", "x"]): ref_copies = ploidy // 2 else: ref_copies = ploidy return ref_copies def _log2_ratio_to_absolute(log2_ratio, ref_copies, expect_copies, purity=None): """Transform a log2 ratio to absolute linear scale (for an impure sample). Does not round to an integer absolute value here. Math:: log2_ratio = log2(ncopies / ploidy) 2^log2_ratio = ncopies / ploidy ncopies = ploidy * 2^log2_ratio With rescaling for purity:: let v = log2 ratio value, p = tumor purity, r = reference ploidy, x = expected ploidy, n = tumor ploidy ("ncopies" above); v = log_2(p*n/r + (1-p)*x/r) 2^v = p*n/r + (1-p)*x/r n*p/r = 2^v - (1-p)*x/r n = (r*2^v - x*(1-p)) / p If purity adjustment is skipped (p=1; e.g. if germline or if scaling for heterogeneity was done beforehand):: n = r*2^v """ if purity and purity < 1.0: ncopies = (ref_copies * 2**log2_ratio - expect_copies * (1 - purity) ) / purity else: ncopies = _log2_ratio_to_absolute_pure(log2_ratio, ref_copies) return ncopies def _log2_ratio_to_absolute_pure(log2_ratio, ref_copies): """Transform a log2 ratio to absolute linear scale (for a pure sample). Purity adjustment is skipped. This is appropriate if the sample is germline or if scaling for tumor heterogeneity was done beforehand. .. math :: n = r*2^v """ ncopies = ref_copies * 2 ** log2_ratio return ncopies
[docs]def rescale_baf(purity, observed_baf, normal_baf=0.5): """Adjust B-allele frequencies for sample purity. Math:: t_baf*purity + n_baf*(1-purity) = obs_baf obs_baf - n_baf * (1-purity) = t_baf * purity t_baf = (obs_baf - n_baf * (1-purity))/purity """ # ENH: use normal_baf array if available tumor_baf = (observed_baf - normal_baf * (1-purity)) / purity # ENH: warn if tumor_baf < 0 -- purity estimate may be too low return tumor_baf