hiReadsProcessor (version 1.8.2)

removeReadsWithNs: Remove sequences with ambiguous nucleotides.

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)