pvca: A function for Principal Variance Component Analysis
In dleelab/leedonghyung: a set of useful R functions
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/leedonghyung documentation built on May 7, 2019, 8:43 a.m.
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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.
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