Given a data matrix, this function will estimate the sequencing depths
on the basis of the Poisson goodness-of-fit statistic.
This estimate is applicable to data with any types of outcome, as it
estimates under the null hypothesis.
A more detailed instruction as well as sample data is available at
http://www.stanford.edu/~junli07/research.html.
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.mean
if the mean number of reads of a gene across all experiments
Value
estimated sequencing depth. a vector. their product is 1.
Details
The value in the data matrix does not need to be integers.
References
Li J, Witten DM, Johnstone I, Tibshirani R (2011).
Normalization, testing, and false discovery rate estimation for RNA-sequencing data.
To appear, Biostatistics.