# Generate Quality Surrogate Variable Analysis for Degradation Correction

## Documentation for package ‘qsvaR’ version 1.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

degradation_tstats | Degradation time t-statistics
DEqual | Differential expression quality (DEqual) plot
getDegTx | Obtain expression matrix for degraded transcripts
getPCs | PCs from transcripts
get_qsvs | Generate matrix of qsvs
k_qsvs | Apply num.sv algorithm to determine the number of pcs to be included
normalize_tx_names | Remove version number from Gencode/Ensembl transcript names
qSVA | A wrapper function used to perform qSVA in one step.
rse_tx | Example of RSE object with RNA-seq transcript quantification data
select_transcripts | Select transcripts associated with degradation
transcripts | Transcripts for Degradation Models
which_tx_names | Check validity of transcript vectors and return a vector matching indexes in tx1