pca.norm: PCA-based normalization of bin counts
In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal
Description
Usage
Arguments
Value
Author(s)
Description
Bin counts are normalized by regressing out the effect of the first Principal
Components. Beforehands, the average coverage is normalized. Then PC are computed
using prcomp function and regressed out using linear regression.
Usage
1
Arguments
bc.df
a data.frame with 'chr', 'start', 'end' columns and then one column per sample with its bin counts.
nb.pcs
the number of Principal Components to include in the regression model.
nb.cores
the number of cores to use. Default is 1.
norm.stats.comp
Should some statistics on the normalized bin count be computed (mean, sd, outliers). Default is TRUE.
Value
a list with
norm.stats
a data.frame witht some metrics about the normalization of each
bin (row) : coverage average and standard deviation; number of outlier reference samples; principal components
bc.norm
a data.frame, similar to the input 'bc.df', with the normalized bin counts.
Author(s)
Jean Monlong
jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.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 Value Author(s)
Description
Bin counts are normalized by regressing out the effect of the first Principal
Components. Beforehands, the average coverage is normalized. Then PC are computed
using prcomp function and regressed out using linear regression.
Usage
1 |
Arguments
bc.df |
a data.frame with 'chr', 'start', 'end' columns and then one column per sample with its bin counts. |
nb.pcs |
the number of Principal Components to include in the regression model. |
nb.cores |
the number of cores to use. Default is 1. |
norm.stats.comp |
Should some statistics on the normalized bin count be computed (mean, sd, outliers). Default is TRUE. |
Value
a list with
norm.stats |
a data.frame witht some metrics about the normalization of each bin (row) : coverage average and standard deviation; number of outlier reference samples; principal components |
bc.norm |
a data.frame, similar to the input 'bc.df', with the normalized bin counts. |
Author(s)
Jean Monlong
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.