Add Filter-2-adjusted depth matrix to a redeemR object

This function reads the “QualifiedTotalCts” matrix from disk (if not already supplied), applies the Filter-2 adjustment—subtracting counts for UMIs removed by edge trimming (zeros and unaffected entries remain unchanged)—then reshapes the result into a matrix matching the dimensions of object@Cts.Mtx.bi and stores it in object@Ctx.Mtx.depth.

Usage

Add_DepthMatrix_filter2(object, QualifiedTotalCts = NULL)

Arguments

object

A redeemR object

QualifiedTotalCts

Optional data.frame of the same format as the “QualifiedTotalCts” file. If NULL, it will be read from file.path(object@attr$path, "QualifiedTotalCts").

Value

The input redeemR object, with object@Ctx.Mtx.depth populated.