se: Example RNA structure probing data set.

In BUMHMM: Computational pipeline for computing probability of modification from structure probing experiment data

Description

A SummarizedExperiment container storing the genomic sequence of the yeast rRNA 18S and three matrices with coverage, drop-off count, and drop-off rate information for each nucleotide position in three replicates of control and treatment DMS structure probing experiments.

Usage

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Format

An instance of the SummarizedExperiment class storing data obtained in a structure probing experiment for the yeast rRNA 18S using the DMS chemical probing agent. The data can be accessed in the Gene Expression Omnibus with the code GSE52878.

The available data types are summarised in three assays: coverage, drop-off count of the reverse transcriptase, and drop-off rate at each nucleotide position. The coverage and drop-off count data are obtained in a random-primed paired-end sequencing structure probing experiment. The drop-off rate is computed as the ratio between the drop-off count and coverage at each nucleotide position. Control (no reagent added) and treatment experiments are available in triplicates.

The data from each assay is summarised in a rectangular matrix. The rows represent nucleotide position and the columns represent experimental replicates. The replicates are labelled as "control" or "treatment", which is stored as column data and can be accessed through the field replicate. The row data stores the associated DNA sequence, represented with a DNAString object.

Details

The SummarizedExperiment object can be created from individual matrices and the sequence string as follows. Below:

seq

a string storing the genomic sequence

covFile

a matrix storing coverage information, with rows as nucleotide positions and columns as experimental replicates (control replicates come first, followed by treatment replicates)

docFile

a matrix storing drop-off count information, arranged as covFile

dorFile

a matrix storing drop-off rate information, arranged as covFile

The seq, covFile, docFile, and dorFile are also provided as accompanying data sets for reference.

Example code:

library(BUMHMM) library(Biostrings) library(SummarizedExperiment)

dna = DNAString(seq) se <- SummarizedExperiment( list( coverage=as.matrix(covFile), dropoff_count=as.matrix(docFile), dropoff_rate=as.matrix(dorFile) ), colData=DataFrame( replicate=rep(c("control", "treatment"), each=3) ), rowData=DataFrame( nucl=Views(dna, successiveIRanges(rep(1, nchar(dna)))) )) colnames(se) <- c('C1', 'C2', 'C3', 'T1', 'T2', 'T3')

Value

RNA structure probing data.

References

Hector, R. D. et al. "Snapshots of pre-rRNA structural flexibility reveal eukaryotic 40S assembly dynamics at nucleotide resolution." Nucleic acids research (2014).

BUMHMM documentation built on Nov. 8, 2020, 5:13 p.m.