Package index • raer

Pileup

pileup_cells(): Generate base counts per cell

pileup_sites() FilterParam(): Generate base counts using pileup

Calculations

calc_AEI(): Calculate the Adenosine Editing Index (AEI)

calc_confidence(): Calculate confidence score for observing editing

calc_edit_frequency(): Adds editing frequencies

calc_scAEI() get_scAEI_sites(): Calculate the Adenosine Editing Index (AEI) in single cells

Filtering

filter_clustered_variants(): Filter out clustered sequence variants

filter_multiallelic(): Filter out multi-allelic sites

filter_splice_variants(): Filter out sites near splice sites

Annotation

annot_from_gr(): Annotate sites using GRanges object

annot_snps(): Annotate known SNP positions

get_overlapping_snps(): Retrieve SNPs overlapping intervals

get_splice_sites(): Extract regions surrounding splice sites

Bulk editing analysis

find_de_sites(): Perform differential editing

make_de_object(): Make summarized experiment object for differential editing analysis

Single cell editing analysis

find_scde_sites(): Identify sites with differential editing between cells in single cell datasets

find_mispriming_sites(): Find regions with oligodT mispriming

Utilities

correct_strand(): Apply strand correction using gene annotations

calc_scAEI() get_scAEI_sites(): Calculate the Adenosine Editing Index (AEI) in single cells

mock_rse(): Generate a small RangedSummarizedExperiment object for tests and examples

raer_example(): Provide working directory for raer example files.

read_sparray(): Read sparseMatrix produced by pileup_cells()