counts_shift {weitrix} | R Documentation |
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.
counts_shift(counts, grouping, verbose = TRUE)
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 |
verbose |
If TRUE, output some debugging and progress information. |
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.
A SummarizedExperiment object with metadata fields marking it as a weitrix.
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)