PoolColumns: Pool reads across columns

In grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Pool reads across columns

Description

Pool read counts, ntrs, and alpha/beta values across columns defined by a pooling matrix

Usage

PoolColumns(
  data,
  pooling = GetSummarizeMatrix(data, average = FALSE, no4sU = TRUE)
)

Arguments

data	grandR object
pooling	a pooling matrix (see details)

Details

The pooling matrix must have as many rows as there are columns (i.e., samples or cells) in data, and as many columns as you want to have columns in the resulting object. The matrix should consist of 0 and 1, where 1 indicates a column of the original object that should go into a column of the new object. In essence, to obtain the new count matrix, the old count matrix is matrix-multiplied with the pooling matrix.

The new ntr matrix is computed by componentwise division of the new count and total count matrices derived as just described. alpha and beta are computed using matrix multiplication, i.e. summing up all alpha and beta values of all the columns belonging to a pool.

Value

a new grandR object

grandR documentation built on April 4, 2025, 2:27 a.m.