subsample: Subsample reads and perform statistical testing on each...
In StoreyLab/subSeq: Subsampling of high-throughput sequencing count data

Description Usage Arguments Details Value Examples

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.

1 2	subsample(counts, proportions, method = "edgeR", replications = 1, seed = NULL, qvalues = TRUE, env = parent.frame(), ...)

`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`

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.

A subsample S3 object, which is a data.table containing

`pvalue`	A p-value calculated for each gene by the handler
`coefficient`	An effect size (usually log fold change) calculated for each gene by the handler
`ID`	gene ID
`count`	the number of reads to this specific gene in this subsample
`depth`	the overall sequencing depth of this subsample
`method`	the method used (the name of the handler)

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"))