Esimate sequencing depth

Functions from PossionSeq (https://doi.org/10.1093/biostatistics/kxr031)

Usage

PS.Est.Depth(n, iter = 5, ct.sum = 5, ct.mean = 0.5)

Arguments

n

The data matrix. The rows are counts for a gene, and the columns are counts from an experiment.

iter

Number of iterations used. Default value: 5. The default value is usually a good choice.

ct.sum

if the total number of reads of a gene across all experiments <= ct.sum, this gene will not be considered for estimating sequencing depth. Default value: 5.

ct.mean

if the mean number of reads of a gene across all experiments <= ct.mean, this gene will not be considered for estimating sequencing depth. Default value: 0.5.

Value

estimated sequencing depth. a vector. their product is 1.

Examples

mat <- matrix(rnbinom(300, mu=100, size=1), ncol=5)
PS.Est.Depth(mat)
#> [1] 1.3929053 1.0767802 0.9736520 0.7609921 0.8998445