Description Usage Arguments Value Author(s)
View source: R/assignQuantityToSP.R
Assigns quantities to predicted subpopulations. Currently, the only assignable quantity are subpopulation specific copy number states for the input genome segments.
1 |
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: |
dm |
Matrix in which each row corresponds to a mutation. Has to contain at least the following column names: |
C |
List referencing column names in the mutation matrix, with two fields: |
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. |
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).
Noemi Andor
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