getVariantPercentages {R453Plus1Toolbox} | R Documentation |
This function computes the coverage for each variant (in forward and/or reverse direction) for all samples. The coverage is defined as the percentual amount of reads that cover a variant.
getVariantPercentages(object, direction="both")
object |
An instance of class |
direction |
A character indicating the direction ("forward", "reverse" or "both"). |
If the direction was set to "both", the percentages are computed over the sum of both directions. Otherwise it is computed only over the
occurences in one direction (forward or reverse). The occurences can be accesses via assayData
.
getVariantPercentages
returns a data frame with all percentages/frequencies for all samples.
Christoph Bartenhagen
# load a (filtered) AVA dataset containing 6 samples, 4 amplicons and 4 variants data(avaSetFiltered) avaSetFiltered # both directions getVariantPercentages(avaSetFiltered, direction="both") # this is equivalent to (assayData(avaSetFiltered)[[1]] + assayData(avaSetFiltered)[[3]]) / (assayData(avaSetFiltered)[[2]] + assayData(avaSetFiltered)[[4]]) # forward direction only getVariantPercentages(avaSetFiltered, direction="forward") # this is equivalent to assayData(avaSetFiltered)[[1]] / assayData(avaSetFiltered)[[2]] # reverse direction only getVariantPercentages(avaSetFiltered, direction="reverse") # this is equivalent to assayData(avaSetFiltered)[[3]] / assayData(avaSetFiltered)[[4]]