srnadiffExp {srnadiff} | R Documentation

## Infrastructure for sRNA-Seq experiment and differential expression

### Description

`srnadiffExp` is an S4 class providing the infrastructure (slots) to store the input data, methods parameters, intermediate calculations and results of a sRNA-diff approach.

### Usage

    srnadiffExp(
      bamFiles = NULL,
      sampleInfo = NULL,
      annotReg = NULL,
      diffMethod = NULL,
      normFactors = NULL
    )

    ## S4 method for signature 'srnadiffExp'
    show(object)

### Arguments

`bamFiles` | A vector with the full paths to the BAM files.
`sampleInfo` | A `data.frame` with three columns labelled `FileName`, `SampleName` and `Condition`. The first column is the BAM file name (without extension), the second column the sample name, and the third column the condition to which sample belongs. Each row describes one sample.
`annotReg` | Optional annotation information. Annotated regions as a `GRanges` object. By example, ranges in the output from `readAnnotation`.
`diffMethod` | A character storing the name of the method used to compute the p-values. Can be `DESeq2` (default), `edgeR`, or `baySeq`.
`normFactors` | A numeric vector, one size factor for each sample in the data.
`object` | An `srnadiffExp` object.

### Details

`srnadiffExp` load and summarize sample BAM files into base-resolution coverage and estimate the size factors (the effective library size) from the coverage data.

To facilitate programming pipelines, `NULL` values are input for `regions`, `parameters` and `countMatrix` slots, in which case the default value is used as if the argument had been missing. These slots will be updated after differential expression (`srnadiff`) approach.

### Value

`srnadiffExp` constructor returns an `srnadiffExp` object of class S4.

The `show` method informatively display object contents.

### Slots

`bamFiles`

  A `BamFileList` object with the full paths to the BAM files.

`sampleInfo`

  A `data.frame` with sample and experimental design information. Each row describes one sample.

`annotReg`

  A `GRanges` with annotation information.

`diffMethod`

  A character storing the name of the method used to compute the p-values. Can be `DESeq2`, `edgeR`, or `baySeq`.

`chromosomeSizes`

  A named vector with the sizes of the chromosomes.

`coverages`

  The sample coverages, a named `RleList` object.

`normFactors`

  A vector of normalization factors.

`regions`

  A `GenomicRanges` of the candidate differentially expressed regions.

`countMatrix`

  A matrix of non-negative integer count values, one row per region and one column per sample.

`parameters`

  An named `list`. The parameters for the segmentation methods. See `parameters`.

### Examples

    basedir    <- system.file("extdata", package="srnadiff", mustWork = TRUE)
    sampleInfo <- read.csv(file.path(basedir, "dataInfo.csv"))
    gtfFile    <- file.path(basedir, "Homo_sapiens.GRCh38.76.gtf.gz")
    annotReg   <- readAnnotation(gtfFile, feature="gene", source="miRNA")
    bamFiles   <- file.path(basedir, sampleInfo$FileName)

    srnaExp <- srnadiffExp(bamFiles, sampleInfo, annotReg)
    srnaExp

[Package srnadiff version 1.14.0 Index]