For a given AVASet, this function imports all aligned reads belonging to all (or some selected) amplicons of all samples.
An instance of the
An (optional) character vector of amplicon names as
mentioned in the amplicon feature data (see
Usually, the method tries to retrieve the path to the AVA
project from the given
This function reports all reads for all samples together. If you want to get the reads for some samples individually, try subsetting your AVASet as in the examples below.
DNAStringSet that contains all aligned reads for all samples (eventually restricted to some given amplicons).
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# load an AVA dataset containing 6 samples, 4 amplicons and 259 variants data(avaSetExample) # import all reads for amplicon "TET2_E11.04" of the first sample avaProjectDir = system.file("extdata", "AVASet", package = "R453Plus1Toolbox") alnReads = getAlignedReads(avaSetExample[, 1], dir=avaProjectDir, amplicons="TET2_E11.04") show(alnReads)
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