Compute c-score for all samples in a riboclass — compute

In this package, the C-score is calculated for every position. As it can be useful to find positions not yet identified as methylated.

This function is called automatically when loading data or after adjusting biases in end read count data with ComBat-seq. It can be still called manually to modify how the C-score is currently computed.

For each RNA, the first and last positions cannot be calculated if the local coverage is shorter than the flanking argument. Their value will be NA instead.

Usage

compute_cscore(ribo = NULL, flanking = 6, method = "median", ncores = 1)

Arguments

ribo: A RiboClass object.
flanking: Size of the local coverage.
method: Computation method of the local coverage. Either 'median' or 'mean'.
ncores: Number of cores to use in case of multithreading.

Value

A RiboClass with c-score columns appended to each sample's data.

References

Birkedal, U., Christensen-Dalsgaard, M., Krogh, N., Sabarinathan, R., Gorodkin, J. and Nielsen, H. (2015), Profiling of Ribose Methylations in RNA by High-Throughput Sequencing. Angew. Chem. Int. Ed., 54: 451-455. https://doi.org/10.1002/anie.201408362

Examples

data('ribo_toy')
ribo_subsetted <- keep_ribo_samples(ribo_toy,'S1')
ribo_with_cscore_med <- compute_cscore(ribo_subsetted, ncores = 2)
ribo_with_cscore_mean <- compute_cscore(ribo_subsetted, method = 'mean', ncores = 2)