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.
1 2 3 | 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 |
an edit_summary object
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