assignQuantityToSP: Quantity assignment (copy number) to subpopulations

In expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations

Description

Assigns quantities to predicted subpopulations. Currently, the only assignable quantity are subpopulation specific copy number states for the input genome segments.

Usage

assignQuantityToSP(cbs, dm, C=list(sp=c("SP","SP_cnv"), pm=c("PM","PM_cnv")), e=1, v=T)

Arguments

cbs	Matrix in which each row corresponds to a copy number fragment as computed by a circular binary segmentation algorithm. Has to contain at least the following column names: chr - chromosome; startpos - the first genomic position of a copy number segment; endpos - the last genomic position of a copy number segment; CN_Estimate - the copy number estimated for each segment (weighted average value across all subpopulations in the sample).
dm	Matrix in which each row corresponds to a mutation. Has to contain at least the following column names: chr - chromosome on which each point mutation is located; startpos - genomic position of each mutation; SP - subpopulation to which the point mutation has been assigned; SP_cnv - subpopulation with a copy number variation within the same genomic segment in which SP has a point mutation; PM - total count of all alleles in the subpopulation with the point mutation (SP); PM_cnv - total count of all alleles in the subpopulation with the copy number variation (SP_cnv).
C	List referencing column names in the mutation matrix, with two fields: sp - column names holding subpopulation sizes (typically "SP", "SP_cnv"); pm - column names holding the total allele counts assigned for each subpopulation (typically "PM", "PM_cnv").
e	Maximum variance of subpopulation specific copy numbers for a given segment, above which segment will remain unassigned for the corresponding subpopulation. Determines whether or not to assign copy number to a subpopulation, SP_i, for a segment containing multiple SP_i specific copy numbers, at least two of which are distinct.
v	Give a more verbose output.

Value

The input copy number matrix with one additional column for each predicted subpopulation:
SP_xx - where xx is the size of the corresponding subpopulation. Column entries contain the copy number of each segment in SP; Value <NA> indicates that no copy number could be inferred for the segment in this subpopulation (either because the subpopulation had no point mutations/CNVs within the segment, or because it had multiple, ambiguous copy number assignments within the segment).

Author(s)

Noemi Andor

expands documentation built on Sept. 5, 2021, 5:18 p.m.