Remove (zero out) CNV data from a qseaSet

Set all per-window CNV values to zero while keeping genomic coordinates and sample metadata intact. Useful for resetting CNV prior to recomputation.

removeCNV(qseaSet)

Arguments

qseaSet

qseaSet. Input object whose CNV assay will be replaced by zeros.

Value

A qseaSet with the CNV matrix zeroed (same dimensions as before).

Details

This operation preserves regions (windows) and sample metadata; only the per-window CNV values are replaced with zeros. Use this to “clear” existing CNV calls before running addHMMcopyCNV() or other CNV routines again.

See also

addHMMcopyCNV(), plotCNVheatmap(), qsea::addCNV()

Other CNV: addHMMcopyCNV(), plotCNVheatmap(), runHMMCopy()

Examples

data(exampleTumourNormal, package = "mesa")

# Zero out CNV and inspect the first rows
exampleTumourNormal %>%
    removeCNV() %>%
    getCNV() %>%
    utils::head()
#> GRanges object with 6 ranges and 10 metadata columns:
#>       seqnames          ranges strand |  Colon1_N  Colon1_T  Colon2_N  Colon2_T
#>          <Rle>       <IRanges>  <Rle> | <numeric> <numeric> <numeric> <numeric>
#>   [1]        1       1-1000000      * |         0         0         0         0
#>   [2]        1 1000001-2000000      * |         0         0         0         0
#>   [3]        1 2000001-3000000      * |         0         0         0         0
#>   [4]        1 3000001-4000000      * |         0         0         0         0
#>   [5]        1 4000001-5000000      * |         0         0         0         0
#>   [6]        1 5000001-6000000      * |         0         0         0         0
#>         Lung1_N   Lung1_T   Lung2_N   Lung2_T   Lung3_N   Lung3_T
#>       <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
#>   [1]         0         0         0         0         0         0
#>   [2]         0         0         0         0         0         0
#>   [3]         0         0         0         0         0         0
#>   [4]         0         0         0         0         0         0
#>   [5]         0         0         0         0         0         0
#>   [6]         0         0         0         0         0         0
#>   -------
#>   seqinfo: 22 sequences from an unspecified genome; no seqlengths