RNA editing tools in R


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Documentation for package ‘raer’ version 1.4.0

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annot_from_gr Annotate sites using GRanges object
annot_snps Annotate known SNP positions
annot_snps.GRanges Annotate known SNP positions
annot_snps.SummarizedExperiment Annotate known SNP positions
calc_AEI Calculate the Adenosine Editing Index (AEI)
calc_confidence Calculate confidence score for observing editing
calc_edit_frequency Adds editing frequencies
calc_scAEI Calculate the Adenosine Editing Index (AEI) in single cells
correct_strand Apply strand correction using gene annotations
FilterParam Generate base counts using pileup
filter_clustered_variants Filter out clustered sequence variants
filter_multiallelic Filter out multi-allelic sites
filter_splice_variants Filter out sites near splice sites
find_de_sites Perform differential editing
find_mispriming_sites Find regions with oligodT mispriming
find_scde_sites Identify sites with differential editing between cells in single cell datasets
get_overlapping_snps Retrieve SNPs overlapping intervals
get_scAEI_sites Calculate the Adenosine Editing Index (AEI) in single cells
get_splice_sites Extract regions surrounding splice sites
make_de_object Make summarized experiment object for differential editing analysis
mock_rse Generate a small RangedSummarizedExperiment object for tests and examples
pileup_cells Generate base counts per cell
pileup_sites Generate base counts using pileup
raer_example Provide working directory for raer example files.
read_sparray Read sparseMatrix produced by pileup_cells()