summarize.intensity: Summarize hybridization intensity by sample
In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays
Description
Usage
Arguments
Details
Value
See Also
Description
Summarize hybridization intensity by sample
Usage
1
summarize.intensity(gty, q = seq(0, 1, 0.1), ..., .progress = "none")
Arguments
gty
a genotypes object with intensity data attached
q
a vector of quantiles (in [0,1])
...
ignored
.progress
show a progress bar; passed through to plyr, see ddply
Details
The qth quantiles of "sum-intensity" are computed for each sample, across all markers
in the input dataset. Missing values are silently ignored. We define "sum-intensity" as
sqrt(x_i^2 + y_i^2), rather than sum(x_i + y_i), based on the intuition that distance from
the origin represents total hybridization intensity after application of Illumina's proprietary
affine-transformation scheme to the raw fluorescences.
Value
a dataframe containing intensity quantiles for each sample, merged with
sample metadata (if present)
See Also
summarize.calls, intensity.vs.ref, run.sample.qc
andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.
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.
Description Usage Arguments Details Value See Also
Description
Summarize hybridization intensity by sample
Usage
1 | summarize.intensity(gty, q = seq(0, 1, 0.1), ..., .progress = "none")
|
Arguments
gty |
a |
q |
a vector of quantiles (in [0,1]) |
... |
ignored |
.progress |
show a progress bar; passed through to |
Details
The qth quantiles of "sum-intensity" are computed for each sample, across all markers
in the input dataset. Missing values are silently ignored. We define "sum-intensity" as
sqrt(x_i^2 + y_i^2), rather than sum(x_i + y_i), based on the intuition that distance from
the origin represents total hybridization intensity after application of Illumina's proprietary
affine-transformation scheme to the raw fluorescences.
Value
a dataframe containing intensity quantiles for each sample, merged with sample metadata (if present)
See Also
summarize.calls, intensity.vs.ref, run.sample.qc
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.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.