makeCountsFromAbundance: Low-level function to make counts from abundance using...
In tximport: Import and summarize transcript-level estimates for transcript- and gene-level analysis
Description
Usage
Arguments
Value
Description
Simple low-level function used within tximport to generate
scaledTPM or lengthScaledTPM counts, taking as input
the original counts, abundance and length matrices.
NOTE: This is a low-level function exported in case it is needed for some reason,
but the recommended way to generate counts-from-abundance is using
tximport with the countsFromAbundance argument.
Usage
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makeCountsFromAbundance(
countsMat,
abundanceMat,
lengthMat,
countsFromAbundance = c("scaledTPM", "lengthScaledTPM")
)
Arguments
countsMat
a matrix of original counts
abundanceMat
a matrix of abundances (typically TPM)
lengthMat
a matrix of effective lengths
countsFromAbundance
the desired type of count-from-abundance output
Value
a matrix of count-scale data generated from abundances.
for details on the calculation see tximport.
tximport documentation built on Nov. 8, 2020, 8:20 p.m.
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Description Usage Arguments Value
Description
Simple low-level function used within tximport to generate
scaledTPM or lengthScaledTPM counts, taking as input
the original counts, abundance and length matrices.
NOTE: This is a low-level function exported in case it is needed for some reason,
but the recommended way to generate counts-from-abundance is using
tximport with the countsFromAbundance argument.
Usage
1 2 3 4 5 6 | makeCountsFromAbundance(
countsMat,
abundanceMat,
lengthMat,
countsFromAbundance = c("scaledTPM", "lengthScaledTPM")
)
|
Arguments
countsMat |
a matrix of original counts |
abundanceMat |
a matrix of abundances (typically TPM) |
lengthMat |
a matrix of effective lengths |
countsFromAbundance |
the desired type of count-from-abundance output |
Value
a matrix of count-scale data generated from abundances. for details on the calculation see tximport.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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