dereplicateReads: Removes duplicate sequences from DNAStringSet object.
In hiReadsProcessor: Functions to process LM-PCR reads from 454/Illumina data
Description
Usage
Arguments
Value
See Also
Examples
View source: R/hiReadsProcessor.R
Description
Given a DNAStringSet object, the function dereplicates reads and
adds counts=X to the definition line to indicate replication.
Usage
1
dereplicateReads(dnaSet)
Arguments
dnaSet
DNAStringSet object to dereplicate.
Value
DNAStringSet object with names describing frequency of repeat.
See Also
replicateReads, removeReadsWithNs,
findBarcodes, splitByBarcode
Examples
1
2
3
4
5
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7
dnaSet <- c("CCTGAATCCTGGCAATGTCATCATC", "ATCCTGGCAATGTCATCATCAATGG",
"ATCAGTTGTCAACGGCTAATACGCG", "ATCAATGGCGATTGCCGCGTCTGCA",
"CCGCGTCTGCAATGTGAGGGCCTAA", "GAAGGATGCCAGTTGAAGTTCACAC",
"CCTGAATCCTGGCAATGTCATCATC", "ATCCTGGCAATGTCATCATCAATGG",
"ATCAGTTGTCAACGGCTAATACGCG", "ATCAATGGCGATTGCCGCGTCTGCA",
"CCGCGTCTGCAATGTGAGGGCCTAA", "GAAGGATGCCAGTTGAAGTTCACAC")
dereplicateReads(dnaSet)
hiReadsProcessor documentation built on Nov. 8, 2020, 5:43 p.m.
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Description Usage Arguments Value See Also Examples
View source: R/hiReadsProcessor.R
Description
Given a DNAStringSet object, the function dereplicates reads and adds counts=X to the definition line to indicate replication.
Usage
1 | dereplicateReads(dnaSet)
|
Arguments
dnaSet |
DNAStringSet object to dereplicate. |
Value
DNAStringSet object with names describing frequency of repeat.
See Also
replicateReads, removeReadsWithNs,
findBarcodes, splitByBarcode
Examples
1 2 3 4 5 6 7 | dnaSet <- c("CCTGAATCCTGGCAATGTCATCATC", "ATCCTGGCAATGTCATCATCAATGG",
"ATCAGTTGTCAACGGCTAATACGCG", "ATCAATGGCGATTGCCGCGTCTGCA",
"CCGCGTCTGCAATGTGAGGGCCTAA", "GAAGGATGCCAGTTGAAGTTCACAC",
"CCTGAATCCTGGCAATGTCATCATC", "ATCCTGGCAATGTCATCATCAATGG",
"ATCAGTTGTCAACGGCTAATACGCG", "ATCAATGGCGATTGCCGCGTCTGCA",
"CCGCGTCTGCAATGTGAGGGCCTAA", "GAAGGATGCCAGTTGAAGTTCACAC")
dereplicateReads(dnaSet)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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