degnorm: Main function to perform degradation normalization.
In DegNorm: DegNorm: degradation normalization for RNA-seq data

Description Usage Arguments Value Examples

degnorm calcualtes the degradation index score for each gene within each sample and return the degradation-normalized read counts.

1 2	degnorm(read_coverage,counts,iteration,loop,down_sampling=1,grid_size=10, cores=1)

`read_coverage`	a list of converage matrices, one per gene
`counts`	dataframe of read counts, each row for one gene, and column for sample. The order and number of genes must match the order in read_coverage matrices.
`iteration`	iteration number for degnorm algorithm. 5 is sufficient.
`loop`	iteration number inside of nonnegative matrix factorization-over approximation. Default is 100.
`down_sampling`	1 for yes (default) and 0 for no. If yes, average coverage score is calcualted on a grid of size specified by grid_size argument. The new coverage matrix formed by the grid average score will be used for baseline selection. This increases the efficiency of algorithm while maintaining comparable accuracy.
`grid_size`	default size is 10 bp.
`cores`	number of cores. Default number if 1. Users should input the maximum possible number of cores for efficiency.

degnorm outputs a list of following objects:

`counts`	a data.drame of read counts for each gene within each sample.
`counts_normed`	a data.drame of degradation-normalized read counts for each gene within each sample.
`DI`	a matrix of degradation index scores for each gene within each sample.
`K`	normalizing scale factor for each gene within each sample after accounting for degradation normalization.
`convergence`	convergence tag; 0 = degnorm was not done on this gene because smaller counts or too short length.1 = degnorm was done with baseline selection. 2 = degnorm done without baseline selection because gene length (after filtering out low count regions)<200 bp. 3= baseline was found, but DI score is too large. 4 = baseline selection didn't coverge.
`envelop`	list of the envelop curves for all genes.

##coverage_res_chr21 is a \code{CoverageClass} object from DegNorm Package.
data(coverage_res_chr21)
res_DegNorm = degnorm(read_coverage = coverage_res_chr21[[1]],
                    counts = coverage_res_chr21[[2]],
                    iteration = 2,
                    down_sampling = 1,
                    grid_size=10,
                    loop = 20,
                    cores=2)