data.binned: An example of binned P-sites data

In jipingw/RiboDiPA: Differential pattern analysis for Ribo-seq data

An example of binned P-sites data

Description

A example data containing binned ribosome P-site tracks of 4 replicates on 885 genes, two biological replicates each for wild type cells and New1 mutant cells, respectively. It is the output of the data binning function dataBinning on P-site coverage data, and input for diffPatternTest function for differential pattern analysis.

Usage

data("data.binned")

Format

A list of 885 matrices corresponding to 885 genes: in each matrix, rows correspond to replicates, columns correspond to bins. Bin names are set to "start-end" genomic coordinates.

Source

The raw data was adapted from Kasari et al 2019.

Examples

data(data.binned)
classlabel <- data.frame(condition = c("mutant", "mutant", 
    "wildtype", "wildtype"), comparison = c(2, 2, 1, 1))
rownames(classlabel) <- c("mutant1", "mutant2", "wildtype1", "wildtype2")
result.pst <- diffPatternTest(data = data.binned, 
    classlabel = classlabel, method = c('gtxr', 'qvalue'))

jipingw/RiboDiPA documentation built on Dec. 10, 2024, 8:46 p.m.