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"""Trivial segmentation: one segment per chromosome (or arm).
Assume the input CopyNumArray has already been split by chromosome and arm (if
the centromere location can be inferred) via CNA.by_arm().
This procedure calculates a single segment's mean and coordinates across the
given array.
"""
import pandas as pd
from ..segmetrics import segment_mean
def segment_none(cnarr):
"""Return a single segment for the given region."""
colnames = ["chromosome", "start", "end", "log2", "gene", "probes"]
rows = [
(
cnarr.chromosome.iat[0],
cnarr.start.iat[0],
cnarr.end.iat[-1],
segment_mean(cnarr),
"-",
len(cnarr),
)
]
table = pd.DataFrame.from_records(rows, columns=colnames)
segarr = cnarr.as_dataframe(table)
segarr.sort_columns()
return segarr
|
