PVCA: A function for principal variance component analysis
In dleelab/pvca: R package for principal variance component analysis
Description
Usage
Arguments
Value
Description
The function is written based on the 'pvcaBatchAssess' function of the PVCA R package
and slightly changed to make it more efficient and flexible for sequencing read counts data.
(http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/manuals/pvca/man/pvca.pdf)
Usage
1
PVCA(counts, meta, threshold, inter)
Arguments
counts
The Normalized(e.g. TMM)/ log-transformed reads count matrix from sequencing data (row:gene/feature, col:sample)
meta
The Meta data matrix containing predictor variables (row:sample, col:predictor)
threshold
The proportion of the variation in read counts explained by top k PCs. This value determines the number of top PCs to be used in pvca.
inter
TRUE/FALSE - include/do not include pairwise interactions of predictors
Value
std.prop.val The vector of proportions of variation explained by each predictor.
dleelab/pvca documentation built on May 15, 2019, 9:15 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 Value
Description
The function is written based on the 'pvcaBatchAssess' function of the PVCA R package and slightly changed to make it more efficient and flexible for sequencing read counts data. (http://watson.nci.nih.gov/bioc_mirror/packages/release/bioc/manuals/pvca/man/pvca.pdf)
Usage
1 | PVCA(counts, meta, threshold, inter)
|
Arguments
counts |
The Normalized(e.g. TMM)/ log-transformed reads count matrix from sequencing data (row:gene/feature, col:sample) |
meta |
The Meta data matrix containing predictor variables (row:sample, col:predictor) |
threshold |
The proportion of the variation in read counts explained by top k PCs. This value determines the number of top PCs to be used in pvca. |
inter |
TRUE/FALSE - include/do not include pairwise interactions of predictors |
Value
std.prop.val The vector of proportions of variation explained by each predictor.
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.