Applied to an ampliconduo data frame, one element of the return value of the ampliconduo function. Generates a plot of freqB over freqA (the read numbers of the same amplicon in both halves A and B of a split sample). For amplicons that have significantly deviating read numbers, i.e. with a p-value or adjusted p-value below a certain treshold, points are colored differently (default: red).
● Data Source:
CranContrib
● Keywords: hplot
● Alias: plotAmpliconduo
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3 images
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Calculates delta (Δ) and delta prime (Δ'), the fraction of amplicon frequencies and amplicons, respectively, with a false discovery rate below a certain threshold θ as a measure of discordance between two amplicon data sets A and B.
● Data Source:
CranContrib
● Keywords: htest
● Alias: discordance.delta
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0 images
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Implements Fisher's exact test to detect amplicons with significant deviating read numbers between two amplicon sets of the same sample. The p-values of the Fisher's exact test are corrected for multiple testing by computation of the false discovery rates q. This function is intended to help identifying reads that may be the results of experimental artefacts. (The calculation can take some time depending on the size of the data sets and the computing power.)
● Data Source:
CranContrib
● Keywords: htest
● Alias: ampliconduo
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1 images
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Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts.
● Data Source:
CranContrib
● Keywords: package
● Alias: AmpliconDuo, AmpliconDuo-package
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2 images
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Returns the indices of those amplicons in an ampliconduo data frame, that passed the applied filter criteria (ampliconduo data frames are filtered using the filter.ampliconduo or filter.ampliconduo.set function).
● Data Source:
CranContrib
● Keywords: list
● Alias: accepted.amplicons
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Marks or removes amplicons from an ampliconduo data frame according to the specified filter criteria.
● Data Source:
CranContrib
● Keywords: manip
● Alias: filter.ampliconduo
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Marks or removes amplicons from each ampliconduo data frame in a list according to the specified filter criteria.
● Data Source:
CranContrib
● Keywords: manip
● Alias: filter.ampliconduo.set
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0 images
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Plots for an ampliconduo data frame probability densities of the odds ratios of amplicon occurences in the two amplicon data sets. The function allows to shift the two extrema (odds ratios OR = 0 and OR = infinity) to the edges of the plot. Plots of multipe ampliconduo data frames are arranged in a 2-dimensional array with shared scales.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: plotORdensity
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4 images
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Called on the return value of the ampliconduo function, a list of ampliconduo data frames. Generates for each ampliconduo data frame a plot with freqB over freqA and arranges them in a 2-dimensional array, whereas plots in the same row and column share the same scale. Points with a p-value or adjusted p-value below a certain treshold are colored differently (default: red) indicating significant deviations of amplicon occurences between the two samples in an ampliconduo data frame.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: plotAmpliconduo.set
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2 images
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