mismatchLabels {CrispRVariants} | R Documentation

## nonindelLabels

### Description

Make variant labels for variants without an insertion or deletion

### Usage

    mismatchLabels(alns, target, ref.seq, regions = NULL, min.pct = 0,
      mismatch.label = "SNV", genome.to.pos = NULL, as.string = TRUE)

### Arguments

`alns` | A GAlignments object, where the aligned sequences should span the reference sequence
`target` | (GRanges(1)) The region for counting mismatches
`ref.seq` | A DNAString object, the sequence for comparison when checking for mismatches. The sequence does not necessarily have to match the mapping reference sequence. Must span all regions if regions are provided.
`regions` | A GRanges object, regions to check for mismatches with coordinates relative to the reference sequence
`min.pct` | (numeric(1), between 0 and 100) Only return SNVs that occur at in least min.pct change, not any change at a position.
`mismatch.label` | (character(1)) Label to append to the start of mismatch strings, if returning as a single string (Default: "SNV:")
`genome.to.pos` | Optional named vector for transforming variant coordinates into another coordinate system (Default: NULL)
`as.string` | Should individual variant labels be pasted into a single comma separated string when one alignment has multiple variants? (Default: TRUE)

### Value

A data frame of sequence indices, genomic position of mismatch and mismatch base

[Package CrispRVariants version 1.10.1 Index]