Correct the ATAC signal bias in a cancer sample using a bulk copy number profile. First, the copy number profile of interest (in granges format) is integrated with the bin sizes provided in the input SingleCellExperiment object. The copy number profile is then divided out of the input counts and averaged across all cells to approximate the amount of atac specific bias. The input counts are then divided by this bias measure to yield corrected counts.
Usage
correct_atac_bias(
sce,
assay_name,
corrected_name = "counts_corrected",
cn_granges = NULL,
granges_signal_colname,
drop_missing_bins = FALSE
)Arguments
- sce
Single cell experiment object
- assay_name
Name of assay to correct
- corrected_name
Name of corrected assay
- cn_granges
GRanges object containing bulk sample copy number information. Only required if data was not already integrated.
- granges_signal_colname
Column in
cn_grangesthat contains the copy number information.- drop_missing_bins
Logical: Drop bins missing information in
cn_granges.