
splitByBarcode
to perform the actual splitting of file by barcode sequences. If supplied with a character vector and reads themselves, the function behaves a bit differently. See the examples.findBarcodes(sampleInfo, sector = NULL, dnaSet = NULL, showStats = FALSE,
returnUnmatched = FALSE, dereplicate = FALSE, alreadyDecoded = FALSE)
read.sampleInfo
, which holds barcodes and sample names per
sector/quadrant/lane or a character vector of barcodes to sample name
associations. Ex: c("ACATCCAT"="Sample1", "GAATGGAT"="Sample2",...)read.seqsFromSector
and parameters defined in sampleInfo object.dereplicateReads
, which appends counts=X to sequence
names/deflines. Default is FALSE. Not applicable for paired end data since
it can cause insyncronicity.read.SeqFolder
is set to reading sample files and not the
sector files, then set this to TRUE. Default is FALSE. Enabling this
parameter skips the barcode detection step and loads the sequence file as is
into the sampleInfo object.splitByBarcode
, dereplicateReads
,
replicateReads
dnaSet <- DNAStringSet(c("read1"="ACATCCATAGAGCTACGACGACATCGACATA",
"read2"="GAATGGATGACGACTACAGCACGACGAGCAGCTACT",
"read3"="GAATGGATGCGCTAAGAAGAGA", "read4"="ACATCCATTCTACACATCT"))
findBarcodes(sampleInfo=c("ACATCCAT"="Sample1", "GAATGGAT"="Sample2"),
dnaSet=dnaSet, showStats=TRUE, returnUnmatched=TRUE)
load(file.path(system.file("data", package = "hiReadsProcessor"),
"FLX_seqProps.RData"))
findBarcodes(seqProps, sector="all", showStats=TRUE)
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