find_edits: Processes VCF files in search for candidate RNA editing...
In funkhou9/editTools: R Package for RNA editing analysis

Description Usage Arguments Value

Must supply two files - one from RNA seq alignments that come from plus strand transcripts (VCF file 1). The other from minus strand transcripts. (VCF file 2).

Each vcf file requires a genomic DNA sample (the first sample listed in the vcf file), along with any number of RNA samples from various tissues.

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find_edits(file_plus, file_minus = NULL, names = character(),
  ex_indel = TRUE, geno_dp = 10, geno_hom = 95, edit_dp = 5,
  strand_bias = 20)

`file_plus`	input filename for VCF file 1.
`file_minus`	input filename for VCF file 2. If only one VCF file provided, it is assumed that the RNA variants in that file all come from plus strand transcripts.
`names`	A character vector specifying the names of RNA samples in the order they appear in the VCF file.
`ex_indel`	logical indicating whether to exclude indels from the scan
`geno_dp`	integer specifying the minimum genotype depth
`geno_hom`	integer ranging from 0 to 1 specifiying the proportion of homozygosity the genotype must exhibit
`edit_dp`	integer specifying the minimum depth required for evidence of RNA editing
`strand_bias`	integer specifying minimum sample Phred-scaled strand bias for an RNA sample to be considered.
`qual`	An integer specifiying the minimum variant QUAL