getEsts: Complexity estimation for ATACseq libraries.
In RamsinghLab/ATACseeker: Utilities for ATACseq QC, differential accessibility, and integration
Description
Usage
Arguments
Details
Value
Description
Estimate the complexity of a library or sample based on unique fragments
using Daley and Smith's implementation of Good-Toulmin rational function
approximation to solve the missing species problem.
Usage
1
Arguments
xx
The fragments or sample of fragments
withCI
Have preseq compute 95 percent confidence intervals for plots?
...
Other arguments to pass on to preseqR
Details
Original functions in preseqR v2.0.1.1 for this were:
preseqR.rfa.curve and preseqR.rfa.species.accum.curve
The new functions as of the version 3.1.2 are:
ds.mincount == preseqR.rfa.curve
ds.mincount.bootstrap == preseqR.rfa.species.accum.curve
The new functions return generators that can have data passed to them
instead of returning a data frame as in version 2.0.1.1.
It is worth noting that these functions return *non-bootstrapped*
fragment estimates but uses the bootstrapped variance estimates to
calculate CI. This is a function of the latest implementation of preseqR.
Value
A data frame with results
RamsinghLab/ATACseeker documentation built on May 8, 2019, 8:05 a.m.
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Description Usage Arguments Details Value
Description
Estimate the complexity of a library or sample based on unique fragments using Daley and Smith's implementation of Good-Toulmin rational function approximation to solve the missing species problem.
Usage
1 |
Arguments
xx |
The fragments or sample of fragments |
withCI |
Have preseq compute 95 percent confidence intervals for plots? |
... |
Other arguments to pass on to preseqR |
Details
Original functions in preseqR v2.0.1.1 for this were: preseqR.rfa.curve and preseqR.rfa.species.accum.curve
The new functions as of the version 3.1.2 are:
ds.mincount == preseqR.rfa.curve ds.mincount.bootstrap == preseqR.rfa.species.accum.curve
The new functions return generators that can have data passed to them instead of returning a data frame as in version 2.0.1.1.
It is worth noting that these functions return *non-bootstrapped* fragment estimates but uses the bootstrapped variance estimates to calculate CI. This is a function of the latest implementation of preseqR.
Value
A data frame with results
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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