mismatch-utils: Tally processing low-level functions

Description Usage Arguments See Also

Description

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

Usage

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## 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


Rariant documentation built on Nov. 1, 2018, 2:25 a.m.