assignQuantityToSP: Quantity assignment (ploidy) to subpopulations

Description

Assigns quantities to predicted subpopulations. Currently, the only assignable quantity are subpopulation specific ploidies for the input genome segments (obtained for example by circular binary segmentation).

Usage

assignQuantityToSP(cbs, dm, colName = "PM_cnv", keepAmbigSeg=FALSE)

Arguments

cbs

Matrix in which each row corrsponds to a copy number fragment as computed by a circular binary segmentation algorithm. Has to contain at least the following columnnames: chr - chromosome; startpos - the first genomic position of a copy numbe

Matrix in which each row corrsponds to a mutation. Has to contain at least the following columnnames: chr - the chromosome on which each point mutation is located; startpos - the genomic position of each mutation; SP - the subpopulat

colName

The subpopulation specific value assigned to each copy number fragment. Possible values: PM_cnv, PM, PM_B. Default: PM_cnv.

keepAmbigSeg

Whether or not to assign ploidy to a subpopulation, $SP_i$, for a segment containing multiple $SP_i$ specific ploidities, at least two of which have distinct magnitudes. If set to TRUE, the median ploidy is assigned as segment ploidy. Setting this paramet

Value

List with two fields:
dmThe input mutation matrix with missing values in column PM imputed from information in copy number matrix when possible.
ploidyThe input copy number matrix with one additional column for each predicted subpopulation: SP_xx - where xx is the size of the corresponding subpopulation (SP). Column entries contain the ploidy of each segment in SP; Value indicates that no ploidy could be inferred for the segment in this subpopulation (either because SP had no point mutations/CNVs within the segment, or because SP had multiple, ambiguous ploidy assignments within the segment).