weitrix_calibrate: Adjust weights row-wise based on given row dispersions
In weitrix: Tools for matrices with precision weights, test and explore weighted or sparse data
Description
Usage
Arguments
Details
Value
Examples
Description
Based on estimated row dispersions, adjust weights in each row.
Usage
1
weitrix_calibrate(weitrix, dispersions)
Arguments
weitrix
A weitrix object, or an object that can be converted to a weitrix
with as_weitrix.
dispersions
A dispersion for each row.
Details
For large numbers of samples this can be based directly
on weitrix_dispersions.
For small numbers of samples, when using limma,
it should be based on a trend-line fitted to known co-variates of
the dispersions.
This can be done using weitrix_calibrate_trend.
Value
A SummarizedExperiment object with metadata fields marking it as a weitrix.
Examples
1
2
3
4
5
6
# Adjust weights so dispersion for each row is exactly 1. This is dubious
# for a small dataset, but would be fine for a dataset with many columns.
comp <- weitrix_components(simwei, p=1, verbose=FALSE)
disp <- weitrix_dispersions(simwei, comp)
cal <- weitrix_calibrate(simwei, disp)
weitrix_dispersions(cal, comp)
weitrix documentation built on Nov. 8, 2020, 8:10 p.m.
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Description Usage Arguments Details Value Examples
Description
Based on estimated row dispersions, adjust weights in each row.
Usage
1 | weitrix_calibrate(weitrix, dispersions)
|
Arguments
weitrix |
A weitrix object, or an object that can be converted to a weitrix
with |
dispersions |
A dispersion for each row. |
Details
For large numbers of samples this can be based directly
on weitrix_dispersions.
For small numbers of samples, when using limma,
it should be based on a trend-line fitted to known co-variates of
the dispersions.
This can be done using weitrix_calibrate_trend.
Value
A SummarizedExperiment object with metadata fields marking it as a weitrix.
Examples
1 2 3 4 5 6 | # Adjust weights so dispersion for each row is exactly 1. This is dubious
# for a small dataset, but would be fine for a dataset with many columns.
comp <- weitrix_components(simwei, p=1, verbose=FALSE)
disp <- weitrix_dispersions(simwei, comp)
cal <- weitrix_calibrate(simwei, disp)
weitrix_dispersions(cal, comp)
|
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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