recountNNLS: NNLS for Tx Abundance Calculation
In JMF47/recountNNLS: Transcript abundance linear modeling from compressed coverage information
Description
Usage
Arguments
Value
Examples
Description
This function applies NNLS to calculate the transcript abundance
from coverage of exonic and junction coverage statistics for samples
annotated in a phenotype matrix created using processPheno().
Usage
1
recountNNLS(pheno, jx_file = NULL, cores = 1)
Arguments
pheno
The table of phenotype information from processPheno().
jx_file
The path to the Rail-RNA junction coverage file if processing sample not already in recount2.
cores
The number of processing cores to use.
Value
Returns an rse object of the estimated number of reads and the associated standard errors.
Each row represents a protein-coding gene, and each column represents a sample in the phenotype matrix.
Examples
1
2
project = 'SRP063581'
pheno = processPheno(project)
JMF47/recountNNLS documentation built on May 28, 2019, 12:42 p.m.
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Description Usage Arguments Value Examples
Description
This function applies NNLS to calculate the transcript abundance from coverage of exonic and junction coverage statistics for samples annotated in a phenotype matrix created using processPheno().
Usage
1 | recountNNLS(pheno, jx_file = NULL, cores = 1)
|
Arguments
pheno |
The table of phenotype information from processPheno(). |
jx_file |
The path to the Rail-RNA junction coverage file if processing sample not already in recount2. |
cores |
The number of processing cores to use. |
Value
Returns an rse object of the estimated number of reads and the associated standard errors. Each row represents a protein-coding gene, and each column represents a sample in the phenotype matrix.
Examples
1 2 | project = 'SRP063581'
pheno = processPheno(project)
|
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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