counts_shift: Produce a weitrix of shift scores

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

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)

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.

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)

weitrix documentation built on Nov. 8, 2020, 8:10 p.m.