XBSeq (version 1.2.2)

estimateRealCount: Preliminary step to estimate the true signal based on observed signal and background noise

Description

Based on the observed signal as well as the background noise, estimate the true signal for each gene.

Usage

estimateRealCount(object)

Arguments

object

A XBSeqDataSet object

Value

A matrix contains the estimated true signal for each gene with the same length as observed signal.

Details

The observed signal can be achieved by using HTSeq to count the reads map to exonic regions. The background noise can be extracted by using HTSeq the second time to count the reads map to non-exonic regions, the regions we defined by excluding potential functional elements. The the underneath true signal is estimated by the simple subtraction of observed signal and background noise. The true signal of genes with background noise larger than observed signal will be assigned as 0.

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

counts

Examples

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