ct.normalizeMedians: Normalize sample abundance estimates by median gRNA counts

View source: R/Normalization.R

ct.normalizeMediansR Documentation

Normalize sample abundance estimates by median gRNA counts


This function normalizes Crispr gRNA abundance estimates by equalizing the median gRNA abundance values after correcting for library size. It does this by converting raw count values to log2 counts per million and optionally adjusting further in the usual way by dividing these values by user-specified library size factors. THis method should be more stable than the endogenous scaling functions used in voom in th especific case of Crispr screens or other cases where the median number of observed counts may be low.


ct.normalizeMedians(eset, lib.size = NULL)



An ExpressionSet containing, at minimum, count data accessible by exprs.


An optional vector of voom-appropriate library size adjustment factors, usually calculated with calcNormFactors and transformed to reflect the appropriate library size. These adjustment factors are interpreted as the total library sizes for each sample, and if absent will be extrapolated from the columnwise count sums of the exprs slot of the eset.


A renormalized ExpressionSet object of the same type as the provided object.


Russell Bainer



#Build the sample key and library sizes for visualization
sk <- ordered(relevel(as.factor(pData(es)$TREATMENT_NAME), 'ControlReference'))
names(sk) <- row.names(pData(es))
ls <- colSums(exprs(es))

es.norm <- ct.normalizeMedians(es, lib.size= ls)
ct.gRNARankByReplicate(es, sampleKey = sk, lib.size= ls)
ct.gRNARankByReplicate(es.norm, sampleKey = sk, lib.size= ls)

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.