counts_shift: Produce a weitrix of shift scores

In pfh/weitrix: Tools for matrices with precision weights, test and explore weighted or sparse data

Produce a weitrix of shift scores

Description

Produce a weitrix of shift scores between -1 and 1. The input is read counts at a collection of peaks (or other features) in a collection of samples. The peaks can be grouped by gene, and are ordered within each gene.

Usage

counts_shift(counts, grouping, verbose = TRUE, typecast = identity)

Arguments

counts	A matrix of read counts. Rows are peaks and columns are samples.
grouping	A data frame defining the grouping of peaks into genes. Should have a column "group" naming the gene and a column "name" naming the peak (corresponding to rownames(counts)). Within each group, peak names should be ordered from 5' to 3' position.
verbose	If TRUE, output some debugging and progress information.
typecast	A function to convert a matrix to a matrix-like type. Applied at the chunk level, before all chunks are rbinded. Allows use of memory-efficient matrix representations.

Details

For a particular gene, a shift score measures measures the tendency of reads to be upstrand (negative) or downstrand (positive) of the average over all samples. Shift scores range between -1 and 1.

Value

A SummarizedExperiment object with metadata fields marking it as a weitrix.

Examples

grouping <- data.frame(
    group=c("A","A","A","B","B"),
    name=c("p1","p2","p3","p4","p5"))

counts <- rbind(
    p1=c(1,2,0),
    p2=c(0,1,0),
    p3=c(1,0,0),
    p4=c(0,0,1),
    p5=c(0,2,1))

wei <- counts_shift(counts, grouping)

weitrix_x(wei)
weitrix_weights(wei)
rowData(wei)

pfh/weitrix documentation built on Dec. 10, 2024, 5:56 p.m.