assignQuantityToMutation: Quantity assignment (copy number) to mutations

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

Description

Assigns a quantity to each mutated locus. Currently, the only assignable quantity is the average copy number (among all cells) of the locus in which the mutation is embedded.

Usage

assignQuantityToMutation(dm, cbs, quantityColumnLabel="CN_Estimate", verbose = T)

Arguments

dm	Matrix in which each row corresponds to a mutation. Has to contain at least the following column names: chr - the chromosome on which each mutation is located; startpos - the genomic position of each mutation.
cbs	Matrix in which each row corresponds to a copy number segment as calculated 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.
quantityColumnLabel	The name of the new column. Valid options are: FPKM, CN_Estimate.
verbose	Give a more verbose output.

Value

dm	The input matrix with three additional columns: quantityID - the ID of the assigned quantity; quantityColumnLabel - the quantity.

Author(s)

Noemi Andor

Examples

data(cbs)
data(snv)
dm=assignQuantityToMutation(snv,cbs,quantityColumnLabel="CN_Estimate")

Example output

OpenJDK 64-Bit Server VM warning: Can't detect primordial thread stack location - find_vma failed
[1] "Assigning copy number to mutations..."
[1] "Finding overlaps for CBS segment 100 out of  120 ..."
[1] "... Done."

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