mismatch-utils: Tally processing low-level functions

In julian-gehring/Rariant: Identification and Assessment of Single Nucleotide Variants through Shifts in Non-Consensus Base Call Frequencies

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

julian-gehring/Rariant documentation built on May 20, 2019, 4:20 a.m.