counts {XBSeq} | R Documentation

## Accessor functions for the 'counts' information in a XBSeqDataSet object.

### Description

The 'counts' function extract a certian assay element from XBSeqDataSet object. The normalized assay element can be extracted by specifying 'normalized = TRUE'.

### Usage

    ## S4 method for signature 'XBSeqDataSet'
    counts(object,slot = 3, normalized = FALSE)

### Arguments

`object` | a XBSeqDataSet
`slot` | a integer value to specify which assay element to extract (default to 3)
`normalized` | whether the normalized assay element should be returned

### Details

counts is a function to access an array elemen which is specified by the end user. The difference between this function and the counts function for `DESeqDataSet` is that this function can be used to access a specific array elememt rather than a pre-defined array element "counts" in the case of `DESeqDataSet`. By default, the first array element contains information of observed signal. The second array element contains information of background noise. The third array element contains information of estimated true signal after calling the function `estimateRealCount`.

### Value

Either normalized or un-normalized assay element

### References

H. I. Chen, Y. Liu, Y. Zou, Z. Lai, D. Sarkar, Y. Huang, et al., "Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads," BMC Genomics, vol. 16 Suppl 7, p. S14, Jun 11 2015.

### See Also

`XBSeqDataSet`, `DESeqDataSet`

### Examples

       data(ExampleData)
       conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
       XB <- XBSeqDataSet(Observed, Background, conditions)
       str(counts(XB, 1))

[Package XBSeq version 1.22.0 Index]