Rariant (version 1.8.3)

mismatchUtils: 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