mismatchUtils {Rariant} | R Documentation

## Tally processing low-level functions

### Description

Functions for processing position-specific base count tables (tallies) and extracting mismatches counts.

### Usage

    ## low-level functions
    selectStrand(x, strand = c("both", "plus", "minus"), idx = 1:ncol(x))

    seqDepth(x)

    callConsensus(counts, verbose = FALSE)

    mismatchCount(counts, consensus, depth = rowSums(counts))

### Arguments

`x` | Input object
`strand` | Which strand to return?
`idx` | Index of bases to consider (leave as is)
`counts` | Count matrix
`verbose` | Show warnings
`consensus` | Consensus sequence
`depth` | Sequencing depth for counts

.

### See Also

comparativeMismatch

[Package Rariant version 1.20.0 Index]