pipeline: A function representing the pipeline of four steps including...
In demic: Dynamic Estimator of Microbial Communities
View source: R/pipeline_core.R
pipeline R Documentation
A function representing the pipeline of four steps
including GC bias correction, sample filtration, PCA and contig filtration
Description
A function representing the pipeline of four steps
including GC bias correction, sample filtration, PCA and contig filtration
Usage
pipeline(Y, i)
Arguments
Y
a matrix of coverages
i
cutoff of filtering samples changes according to parameter i; i=1, cutoffRatio is 0.5; i=2, cutoffRatio is 1 as contig is clean
Value
a named list
samples: final list of filtered samples
correct_ys: dataframe with correct Y values per contig/sample
pc1: PC1 results of PCA per contig
pc1_range: range of PC1
samples_y: samples filtered for reliable coverage
demic documentation built on May 29, 2024, 10:05 a.m.
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View source: R/pipeline_core.R
| pipeline | R Documentation |
A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtration
Description
A function representing the pipeline of four steps including GC bias correction, sample filtration, PCA and contig filtration
Usage
pipeline(Y, i)
Arguments
Y |
a matrix of coverages |
i |
cutoff of filtering samples changes according to parameter i; i=1, cutoffRatio is 0.5; i=2, cutoffRatio is 1 as contig is clean |
Value
a named list
samples: final list of filtered samples
correct_ys: dataframe with correct Y values per contig/sample
pc1: PC1 results of PCA per contig
pc1_range: range of PC1
samples_y: samples filtered for reliable coverage
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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