Description Usage Arguments Details Value Author(s)
Normalises and performs technical noise analysis for single cell RNAseq(Brennecke et al.)
1 2 3 |
object |
SCD class |
useERCC |
Default TRUE. To use ERCC for technical noise estimation. |
cvThresh |
Defalt 0.3. The CV threshold to use for choosing cells to fit. See quant. |
quant |
Default 0.8. The quantile of data to fit so that linear model is not fitted to plateau at lower gene expression values. See Breenecke et al. for further details |
minBiolDisp |
Default 0.25. Assumed biological dispersion. See paper. |
fdr |
Deafult .1. False Discovery Rate for chi-squared test. |
data.lengths |
Gene lengths in kilobases for PK "per kilobase normalisation" |
ercc.lengths |
ERCC lengths in kilobases for PK "per kilobase normalisation" |
meanForFit |
Provide a minimum mean for fit. (OPTIONAL) |
Normalises and performs a technical noise analysis for single cell RNAseq. Give raw counts. Data is normalised using size-factor normalisation identical to DESeq2, then a technical noise analysis is perfromed as described in brennecke et al.
Returns updated SCD
Wajid Jawaid
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