subsample

0th

Percentile

Subsample reads and perform statistical testing on each sample

Perform subsampling at multiple proportions on a matrix of count data representing mapped reads across multiple samples in many genes. For each sample, perform some statistical operations.

Usage
subsample(counts, proportions, method = "edgeR", replications = 1,
  seed = NULL, qvalues = TRUE, env = parent.frame(), ...)
Arguments
counts
Matrix of unnormalized counts
proportions
Vector of subsampling proportions in (0, 1]
method
One or more methods to be performed at each subsample, such as edgeR or DESeq (see Details)
replications
Number of replications to perform at each depth
seed
An initial seed, which will be stored in the output so that any individual simulation can be reproduced.
qvalues
Whether q-values should be calculated for multiple hypothesis test correction at each subsample.
env
Environment in which to find evaluate additional hander functions that are given by name
...
Other arguments given to the handler, such as treatment
Details

Method represents the name of a handler function, which can be custom-written by the user.

If a gene has a count of 0 at a particular depth, we set the p-value to 1 and the coefficient to 0 to stay consistent between programs. If the gene has a count that is not 0 but the p-value is NA, we set the p-value to 1 but keep the estimated coefficient.

Value

  • A subsample S3 object, which is a data.table containing
  • pvalueA p-value calculated for each gene by the handler
  • coefficientAn effect size (usually log fold change) calculated for each gene by the handler
  • IDgene ID
  • countthe number of reads to this specific gene in this subsample
  • depththe overall sequencing depth of this subsample
  • methodthe method used (the name of the handler)

Aliases
  • subsample
Examples
data(hammer)

hammer.counts = Biobase::exprs(hammer)[, 1:4]
hammer.design = Biobase::pData(hammer)[1:4, ]
hammer.counts = hammer.counts[rowSums(hammer.counts) >= 5, ]

ss = subsample(hammer.counts, c(.01, .1, 1), treatment=hammer.design$protocol,
                 method=c("edgeR", "DESeq2", "voomLimma"))
Documentation reproduced from package subSeq, version 1.2.2, License: MIT + file LICENSE

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