Description Usage Arguments Value Examples
This function extracts estimates for a given model from a list
over many genes, returning a matrix with dimensions:
number of transcript x number of samples.
Here, the count of compatible fragments aligning to the
genes is used to estimate the FPKM, dividing out the previously
used estimate lib.sizes
.
1 2 | extractAlpine(res, model, lib.sizes = 1e+06, divide.out = TRUE,
transcripts = NULL)
|
res |
a list where each element is the output of estimateAbundance |
model |
the name of a model, corresponds to names of |
lib.sizes |
the vector of library sizes passed to estimateAbundance.
not needed if |
divide.out |
logical, whether to divide out the initial estimate of library size and to instead use the count of compatible fragments for genes calculated by estimateAbundance. Default is TRUE |
transcripts |
an optional GRangesList of the exons for each
transcript. If this is provided, the output will be a
SummarizedExperiment. The transcripts do not need
to be provided in the correct order, extractAlpine will
find the correct transcript by the names in |
a matrix of FPKM values across transcripts and samples,
or a SummarizedExperiment if transcripts
is provided
1 2 | data(preprocessedData)
extractAlpine(res, "GC")
|
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