subsample {subSeq} | R Documentation

## Subsample reads and perform statistical testing on each sample

### Description

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

`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)

### 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"))

[Package subSeq version 1.18.0 Index]