geneSitesPhi_from_beta
geneSitesPhi_from_beta.Rdcompute phi for exons in a gene from a Splice object
Usage
geneSitesPhi_from_beta(
spliceOb,
gene,
cells = "all",
mean_psi_lwr = 0.01,
mean_psi_upr = 0.99,
cell_count_thresh = 20,
exprs_thresh = 5,
CI_level = 0.05
)Arguments
- spliceOb
the Splice object
- gene
name of the target gene
- cells
cells to use in building exon count table
- cell_count_thresh
the minimum number of cells expressing this gene
- exprs_thresh
the minimum gene expression to calculate the exon psi (for unbiased estimation)
- CI_level
The alpha for the confidence interval of phi estimation
- exon_len_thresh
the minimum length of an exon to be preserved in exon count table