removeReadsWithNs: Remove sequences with ambiguous nucleotides.

In malnirav/hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data

Description

Given a DNAStringSet object, the function removes any reads that has either repeating or total Ns which is greater than to maxNs threshold

Usage

removeReadsWithNs(dnaSet, maxNs = 5, consecutive = TRUE)

Arguments

dnaSet	DNAStringSet object to evaluate.
maxNs	integer value denoting the threshold of maximum allowed Ns. Default is 5.
consecutive	boolean flag denoting whether Ns to filter is consecutive or total . Default is TRUE.

Value

DNAStringSet object.

See Also

dereplicateReads, replicateReads, findBarcodes, splitByBarcode

Examples

 
dnaSet <- c("CCTGAATCCTNNCAATGTCATCATC", "ATCCTGGCNATGTCATCATCAATGG", 
"ATCAGTTGTCAACGGCTAATACGCG", "ATCAATGGCGATTGCCGCGTCTGCA", 
"CCGNNTCTGCAATGTGNGGNCCTAN", "GAAGNNNNNNGTTGAAGTTCACAC") 
removeReadsWithNs(dnaSet)
removeReadsWithNs(dnaSet, maxNs = 4, consecutive = FALSE)

malnirav/hiReadsProcessor documentation built on July 29, 2021, 6:33 a.m.