ct.GCbias: Visualization of gRNA GC Content Trends
This function visualizes relationships between gRNA GC content and their measured abundance or
various differential expression model estimates.
(data.obj, , sampleKey = , lib.size = )
ExpressionSet or fit (
MArrayLM) object to be analyzed for the presence of GC
data.frame, used to estimate GC content for each guide. Guides are annotated by
row, and the object must minimally contain a
target column containing a character
vector that indicates the corresponding nucleotide sequences.
An optional sample key, supplied as a factor linking the samples to experimental
names attribute should exactly match those present in
eset, and the
control set is assumed to be the first
level. Ignored in the analysis of model fit objects.
An optional vector of voom-appropriate library size adjustment factors, usually calculated with
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
An image relating GC content to experimental observations on the default device. If the
data.obj is an
ExpressionSet, this takes the form of a scatter plot where the
with a smoothed trendline within each sample. If
data.obj is a fit object describing a linear model
contrast, then four panels are returned describing the GC content distribution and its relationship
to guide-level fold change, standard deviation, and P-value estimates.