Compute CNV intensity of gain or loss

This function is used to compute intensity of gain or loss of copies along the transcriptome. For a given position, the intensity is A x B where A the sum of all anomalies (gain or loss) and B is the number of cells having more than +/- 0.075 anomalies at this position. TO DO : - identify the impact of 0.075 - identify the impact the threshold on anomalies detection - below which number of cells an anomaly won't be detected ?

Usage

cnv_compute_intensity(
  table_cnv,
  what = "gain",
  noise_thresh = 0.075,
  contrib_fun = sum
)

Arguments

table_cnv

DATAFRAME : dataframe (genes x cells) containing CNV. Genes must be in the transcriptome order (no default).

what

CHARACTER : either "gain" or "loss" (default to "gain")

noise_thresh

NUMERIC : a threshold above (or below) which a cell is said to carry an anomaly at a specific region. It is used to compute intensity from table_cnv. Value close to 0 will increase the background. It must be in range(table_cnv). If what = "gain", noise_thresh > 0, and if what = "loss", noise_thresh < 0 (default to 0.075)

contrib_fun

FUNCTION : function to compute cells contribution to CNV. It could be sum, mean... of cells having a value above noise_thresh (default to sum)

Value

A vector of length nrow(table_cnv) with intensity of 'what'