bsjExonStats: Calculate exon statistics

In KasperThystrup/circulaR: Characterization of circRNAs from Total RNA-seq data

Description

bsjExonStats determines which circRNAs covers exons of the transcript models provided through the annot argument, and calculates overall statistics for the circRNAs in the input circSample or circExperiment object. The circRNA size are calculated from splicing exons, and covered exons are counted. overlapping exons in a given transcript model is merged, and in case of a circRNA covering multiple transcritp model, the largest size is calculated and selected. Be patient: It currently take minutes to complete when ncores = 5.

plotExonStats Plots crude histograms of the overall statistics calculated for exons from transcript models, covered by detected circRNAs.

Usage

bsjExonStats(object, ...)

## S4 method for signature 'circSample'
bsjExonStats(object, annot, ncores = 4, ...)

## S4 method for signature 'circExperiment'
bsjExonStats(object, annot, ...)

plotExonStats(stats, size_limit = NULL, count_limit = NULL, ...)

Arguments

object	A circSample or circExperiment object
...
annot	The annotation object, either as an EnsDb object or a pre defined exons by transcript CompressedGRangesList object, generated from running exonsBy(x = annot, by = "tx")
ncores	The number of threads (must be a whole number)
stats	plotExonStats: Output from bsjExonStats
size_limit	plotExonStats: Collapse data points where the exonic size is higher thatn the given limit. When NULL (default) data is not collapsed.
count_limit	plotExonStats: Collapse data points where the exonic count is higher thatn the given limit. When NULL (default) data is not collapsed.

Value

Generates histograms over the exon statistics

Author(s)

Kasper Thystrup Karstensen

Examples

# Execute with circSample object using default threading (4 cores)
ahdb <- AnnotationHub()[["AH64923"]]  #  Ensembl Homo sapiens release-94
bsjExonStats(object = circ_smpl, annot = ahdb)

# Exons by transcripts can be used as annotation object
ahdb <- AnnotationHub()[["AH64923"]]
ex_tx <- exonsBy(x = ahdb, by = "tx")
bsjExonStats(object = circ_smpl, annot = ex_tx)

# Execute with circExperiment object using 10 cores
bsjExonStats(object = circ_exp, annot = ahdb, ncores = 10L)

stats <- bsjExonStats(object = circ_exp, annot = ahdb, ncores = 10L)
# Collapse circRNAs with exon sizes > 2000 and exon counts > 10, into a single column.
plotExonStats(stats, size_limit = 2000, count_limit = 10)

# Return a list of ggplot object
p <- plotExonStats(stats)

KasperThystrup/circulaR documentation built on March 14, 2021, 12:44 p.m.