counts_shift {weitrix} | R Documentation

## 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)

### 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)

[Package weitrix version 1.0.0 Index]