counts_proportions: Produce a weitrix of proportions within groups

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

Produce a weitrix of proportions within groups

Description

Produce a weitrix of proportions between 0 and 1. The input is read counts at a collection of features in a collection of samples. The features need to be grouped, for example by gene. The proportions will add to 1 within each group.

Usage

counts_proportions(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 features. Should have a column "group" naming the group and a column "name" naming the feature (corresponding to rownames(counts)).
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.

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_proportions(counts, grouping)

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

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