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apply_CNV_reference

apply_CNV_reference.Rd

Add reference vector to CNV matrix

Usage

apply_CNV_reference(
  cnv = NULL,
  cnv_clustering = NULL,
  reference = "reference",
  eps = 0.2,
  method = c("mean", "min_max")
)

Arguments

cnv

the output of calculate_CNV

cnv_clustering

the output of cluster_by_features(..., cnv=TRUE, ...)

reference

name of the reference column

eps

threshold for the min_max method

method

"mean" (default): subtract the average profile of the reference cluster to every cell; "min_max" see Tirosh et al. (DOI: 10.1126/science.aad0501). In the "min_max" method all values below (above) the maximum (minimum) of the reference cluster + (-) eps are set to 0. The lower (upper) extreme whisker are considered as minimum (maximum) values.